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BCFTOOLS(1)							   BCFTOOLS(1)

NAME
       bcftools - utilities for variant calling and manipulating VCFs and
       BCFs.

SYNOPSIS
       bcftools [--version|--version-only] [--help] [COMMAND] [OPTIONS]

DESCRIPTION
       BCFtools is a set of utilities that manipulate variant calls in the
       Variant Call Format (VCF) and its binary counterpart BCF. All commands
       work transparently with both VCFs and BCFs, both uncompressed and
       BGZF-compressed.

       Most commands accept VCF, bgzipped VCF and BCF with filetype detected
       automatically even when streaming from a pipe. Indexed VCF and BCF will
       work in all situations. Un-indexed VCF and BCF and streams will work in
       most, but not all situations. In general, whenever multiple VCFs are
       read simultaneously, they must be indexed and therefore also
       compressed.

       BCFtools is designed to work on a stream. It regards an input file "-"
       as the standard input (stdin) and outputs to the standard output
       (stdout). Several commands can thus be combined with Unix pipes.

   VERSION
       This manual page was last updated 2015-12-15 14:02 GMT and refers to
       bcftools git version 1.2-191-g6737c5c+.

   BCF1
       The BCF1 format output by versions of samtools <= 0.1.19 is not
       compatible with this version of bcftools. To read BCF1 files one can
       use the view command from old versions of bcftools packaged with
       samtools versions <= 0.1.19 to convert to VCF, which can then be read
       by this version of bcftools.

	       samtools-0.1.19/bcftools/bcftools view file.bcf1 | bcftools view

   VARIANT CALLING
       See bcftools call for variant calling from the output of the samtools
       mpileup command. In versions of samtools <= 0.1.19 calling was done
       with bcftools view. Users are now required to choose between the old
       samtools calling model (-c/--consensus-caller) and the new multiallelic
       calling model (-m/--multiallelic-caller). The multiallelic calling
       model is recommended for most tasks.

LIST OF COMMANDS
       For a full list of available commands, run bcftools without arguments.
       For a full list of available options, run bcftools COMMAND without
       arguments.

       ·    annotate .. edit VCF files, add or remove annotations

       ·    call .. SNP/indel calling (former "view")

       ·    cnv .. Copy Number Variation caller

       ·    concat .. concatenate VCF/BCF files from the same set of samples

       ·    consensus .. create consensus sequence by applying VCF variants

       ·    convert .. convert VCF/BCF to other formats and back

       ·    filter .. filter VCF/BCF files using fixed thresholds

       ·    gtcheck .. check sample concordance, detect sample swaps and
	   contamination

       ·    index .. index VCF/BCF

       ·    isec .. intersections of VCF/BCF files

       ·    merge .. merge VCF/BCF files files from non-overlapping sample
	   sets

       ·    norm .. normalize indels

       ·    plugin .. run user-defined plugin

       ·    polysomy .. detect contaminations and whole-chromosome aberrations

       ·    query .. transform VCF/BCF into user-defined formats

       ·    reheader .. modify VCF/BCF header, change sample names

       ·    roh .. identify runs of homo/auto-zygosity

       ·    stats .. produce VCF/BCF stats (former vcfcheck)

       ·    view .. subset, filter and convert VCF and BCF files

LIST OF SCRIPTS
       Some helper scripts are bundled with the bcftools code.

       ·    plot-vcfstats .. plots the output of stats

COMMANDS AND OPTIONS
   Common Options
       The following options are common to many bcftools commands. See usage
       for specific commands to see if they apply.

       FILE
	   Files can be both VCF or BCF, uncompressed or BGZF-compressed. The
	   file "-" is interpreted as standard input. Some tools may require
	   tabix- or CSI-indexed files.

       -c, --collapse snps|indels|both|all|some|none|id
	   Controls how to treat records with duplicate positions and defines
	   compatible records across multiple input files. Here by
	   "compatible" we mean records which should be considered as
	   identical by the tools. For example, when performing line
	   intersections, the desire may be to consider as identical all sites
	   with matching positions (bcftools isec -c all), or only sites with
	   matching variant type (bcftools isec -c snps	 -c indels), or only
	   sites with all alleles identical (bcftools isec -c none).

	   none
	       only records with identical REF and ALT alleles are compatible

	   some
	       only records where some subset of ALT alleles match are
	       compatible

	   all
	       all records are compatible, regardless of whether the ALT
	       alleles match or not. In the case of records with the same
	       position, only the first will be considered and appear on
	       output.

	   snps
	       any SNP records are compatible, regardless of whether the ALT
	       alleles match or not. For duplicate positions, only the first
	       SNP record will be considered and appear on output.

	   indels
	       all indel records are compatible, regardless of whether the REF
	       and ALT alleles match or not. For duplicate positions, only the
	       first indel record will be considered and appear on output.

	   both
	       abbreviation of "-c indels  -c snps"

	   id
	       only records with identical ID column are compatible. Supported
	       by bcftools merge only.

       -f, --apply-filters LIST
	   Skip sites where FILTER column does not contain any of the strings
	   listed in LIST. For example, to include only sites which have no
	   filters set, use -f .,PASS.

       -o, --output FILE
	   When output consists of a single stream, write it to FILE rather
	   than to standard output, where it is written by default.

       -O, --output-type b|u|z|v
	   Output compressed BCF (b), uncompressed BCF (u), compressed VCF
	   (z), uncompressed VCF (v). Use the -Ou option when piping between
	   bcftools subcommands to speed up performance by removing unecessary
	   compression/decompression and VCF←→BCF conversion.

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   Comma-separated list of regions, see also -R, --regions-file. Note
	   that -r cannot be used in combination with -R.

       -R, --regions-file FILE
	   Regions can be specified either on command line or in a VCF, BED,
	   or tab-delimited file (the default). The columns of the
	   tab-delimited file are: CHROM, POS, and, optionally, POS_TO, where
	   positions are 1-based and inclusive. Uncompressed files are stored
	   in memory, while bgzip-compressed and tabix-indexed region files
	   are streamed. Note that sequence names must match exactly, "chr20"
	   is not the same as "20". Also note that chromosome ordering in FILE
	   will be respected, the VCF will be processed in the order in which
	   chromosomes first appear in FILE. However, within chromosomes, the
	   VCF will always be processed in ascending genomic coordinate order
	   no matter what order they appear in FILE. Note that overlapping
	   regions in FILE can result in duplicated out of order positions in
	   the output. This option requires indexed VCF/BCF files. Note that
	   -R cannot be used in combination with -r.

       -s, --samples [^]LIST
	   Comma-separated list of samples to include or exclude if prefixed
	   with "^". Note that in general tags such as INFO/AC, INFO/AN, etc
	   are not updated to correspond to the subset samples.	 bcftools view
	   is the exception where some tags will be updated (unless the -I,
	   --no-update option is used; see bcftools view documentation). To
	   use updated tags for the subset in another command one can pipe
	   from view into that command. For example:

	       bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n

       -S, --samples-file FILE
	   File of sample names to include or exclude if prefixed with "^".
	   One sample per line. See also the note above for the -s, --samples
	   option. The command bcftools call accepts an optional second column
	   indicating ploidy (0, 1 or 2) or sex (as defined by --ploidy, for
	   example "F" or "M"), and can parse also PED files. If the second
	   column is not present, the sex "F" is assumed. With bcftools call
	   -C trio, PED file is expected. File formats examples:

	       sample1	  1
	       sample2	  2
	       sample3	  2

	     or

	       sample1	  M
	       sample2	  F
	       sample3	  F

	     or a .ped file (here is shown a minimum working example, the first column is
	     ignored and the last indicates sex: 1=male, 2=female)

	       ignored daughterA fatherA motherA 2
	       ignored sonB fatherB motherB 1

       -t, --targets [^]chr|chr:pos|chr:from-to|chr:from-[,...]
	   Similar as -r, --regions, but the next position is accessed by
	   streaming the whole VCF/BCF rather than using the tbi/csi index.
	   Both -r and -t options can be applied simultaneously: -r uses the
	   index to jump to a region and -t discards positions which are not
	   in the targets. Unlike -r, targets can be prefixed with "^" to
	   request logical complement. For example, "^X,Y,MT" indicates that
	   sequences X, Y and MT should be skipped. Yet another difference
	   between the two is that -r checks both start and end positions of
	   indels, whereas -t checks start positions only. Note that -t cannot
	   be used in combination with -T.

       -T, --targets-file [^]FILE
	   Same -t, --targets, but reads regions from a file. Note that -T
	   cannot be used in combination with -t.

	   With the call -C alleles command, third column of the targets file
	   must be comma-separated list of alleles, starting with the
	   reference allele. Note that the file must be compressed and index.
	   Such a file can be easily created from a VCF using:

	       bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz

       --threads INT
	   Number of output compression threads to use in addition to main
	   thread. Only used when --output-type is b or z. Default: 0.

   bcftools annotate [OPTIONS] FILE
       This command allows to add or remove annotations.

       -a, --annotations file
	   Bgzip-compressed and tabix-indexed file with annotations. The file
	   can be VCF, BED, or a tab-delimited file with mandatory columns
	   CHROM, POS (or, alternatively, FROM and TO), optional columns REF
	   and ALT, and arbitrary number of annotation columns. BED files are
	   expected to have the ".bed" or ".bed.gz" suffix (case-insensitive),
	   otherwise a tab-delimited file is assumed. Note that in case of
	   tab-delimited file, the coordinates POS, FROM and TO are one-based
	   and inclusive. When REF and ALT are present, only matching VCF
	   records will be annotated. When multiple ALT alleles are present in
	   the annotation file (given as comma-separated list of alleles), at
	   least one must match one of the alleles in the corresponding VCF
	   record. Similarly, at least one alternate allele from a
	   multi-allelic VCF record must be present in the annotation file.
	   Note that flag types, such as "INFO/FLAG", can be annotated by
	   including a field with the value "1" to set the flag, "0" to remove
	   it, or "." to keep existing flags. See also -c, --columns and -h,
	   --header-lines.

	       # Sample annotation file with columns CHROM, POS, STRING_TAG, NUMERIC_TAG
	       1  752566  SomeString	  5
	       1  798959  SomeOtherString 6
	       # etc.

       -c, --columns list
	   Comma-separated list of columns or tags to carry over from the
	   annotation file (see also -a, --annotations). If the annotation
	   file is not a VCF/BCF, list describes the columns of the annotation
	   file and must include CHROM, POS (or, alternatively, FROM and TO),
	   and optionally REF and ALT. Unused columns which should be ignored
	   can be indicated by "-". If the annotation file is a VCF/BCF, only
	   the edited columns/tags must be present and their order does not
	   matter. The columns ID, QUAL, FILTER, INFO and FORMAT can be
	   edited, where INFO tags can be written both as "INFO/TAG" or simply
	   "TAG", and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
	   To carry over all INFO annotations, use "INFO". To add all INFO
	   annotations except "TAG", use "^INFO/TAG". By default, existing
	   values are replaced. To add annotations without overwriting
	   existing values (that is, to add missing tags or add values to
	   existing tags with missing values), use "+TAG" instead of "TAG". To
	   append to existing values (rather than replacing or leaving
	   untouched), use "=TAG" (instead of "TAG" or "+TAG"). To replace
	   only existing values without modifying missing annotations, use
	   "-TAG". If the annotation file is not a VCF/BCF, all new
	   annotations must be defined via -h, --header-lines.

       -e, --exclude EXPRESSION
	   exclude sites for which EXPRESSION is true. For valid expressions
	   see EXPRESSIONS.

       -h, --header-lines file
	   Lines to append to the VCF header, see also -c, --columns and -a,
	   --annotations. For example:

	       ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
	       ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">

       -I, --set-id [+]FORMAT
	   assign ID on the fly. The format is the same as in the query
	   command (see below). By default all existing IDs are replaced. If
	   the format string is preceded by "+", only missing IDs will be set.
	   For example, one can use

	       bcftools annotate --set-id +'%CHROM\_%POS\_%REF\_%FIRST_ALT' file.vcf

       -i, --include EXPRESSION
	   include only sites for which EXPRESSION is true. For valid
	   expressions see EXPRESSIONS.

       -m, --mark-sites TAG
	   annotate sites which are present ("+") or absent ("-") in the -a
	   file with a new INFO/TAG flag

       -o, --output FILE
	   see Common Options

       -O, --output-type b|u|z|v
	   see Common Options

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       --rename-chrs file
	   rename chromosomes according to the map in file, with "old_name
	   new_name\n" pairs separated by whitespaces, each on a separate
	   line.

       -s, --samples [^]LIST
	   subset of samples to annotate, see also Common Options

       -S, --samples-file FILE
	   subset of samples to annotate. If the samples are named differently
	   in the target VCF and the -a, --annotations VCF, the name mapping
	   can be given as "src_name dst_name\n", separated by whitespaces,
	   each pair on a separate line.

       --threads INT
	   see Common Options

       -x, --remove list
	   List of annotations to remove. Use "FILTER" to remove all filters
	   or "FILTER/SomeFilter" to remove a specific filter. Similarly,
	   "INFO" can be used to remove all INFO tags and "FORMAT" to remove
	   all FORMAT tags except GT. To remove all INFO tags except "FOO" and
	   "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and
	   FILTER). "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".

       Examples:

	       # Remove three fields
	       bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz

	       # Remove all INFO fields and all FORMAT fields except for GT and PL
	       bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf

	       # Add ID, QUAL and INFO/TAG, not replacing TAG if already present
	       bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf

	       # Carry over all INFO and FORMAT annotations except FORMAT/GT
	       bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf

	       # Annotate from a tab-delimited file with six columns (the fifth is ignored),
	       # first indexing with tabix. The coordinates are 1-based.
	       tabix -s1 -b2 -e2 annots.tab.gz
	       bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf

	       # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
	       tabix -s1 -b2 -e3 annots.tab.gz
	       bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf

	       # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
	       bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf

   bcftools cnv [OPTIONS] FILE
       Copy number variation caller, requires a VCF annotated with the
       Illumina’s B-allele frequency (BAF) and Log R Ratio intensity (LRR)
       values. The HMM considers the following copy number states: CN 2
       (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy
       gain).

       General Options:
	   -c, --control-sample string
	       optional control sample name. If given, pairwise calling is
	       performed and the -P option can be used

	   -f, --AF-file file
	       read allele frequencies from a tab-delimited file with the
	       columns CHR,POS,REF,ALT,AF

	   *-o, --output-dir path
	       output directory

	   *-p, --plot-threshold float
	       call matplotlib to produce plots for chromosomes with quality
	       at least float, useful for visual inspection of the calls. With
	       -p 0, plots for all chromosomes will be generated. If not
	       given, a matplotlib script will be created but not called.

	   -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -R, --regions-file file
	       see Common Options

	   -s, --query-sample string
	       query samply name

	   -t, --targets LIST
	       see Common Options

	   -T, --targets-file FILE
	       see Common Options

       HMM Options:
	   -a, --aberrant float[,float]
	       fraction of aberrant cells in query and control. The hallmark
	       of duplications and contaminations is the BAF value of
	       heterozygous markers which is dependent on the fraction of
	       aberrant cells. Sensitivity to smaller fractions of cells can
	       be increased by setting -a to a lower value. Note however, that
	       this comes at the cost of increased false discovery rate.

	   -b, --BAF-weight float
	       relative contribution from BAF

	   d, --BAF-dev float[,float]
	       expected BAF deviation in query and control, i.e. the noise
	       observed in the data.

	   -e, --err-prob float
	       uniform error probability

	   -l, --LRR-weight float
	       relative contribution from LRR. With noisy data, this option
	       can have big effect on the number of calls produced. In truly
	       random noise (such as in simulated data), the value should be
	       set high (1.0), but in the presence of systematic noise when
	       LRR are not informative, lower values result in cleaner calls
	       (0.2).

	   -L, --LRR-smooth-win int
	       reduce LRR noise by applying moving average given this window
	       size

	   -O, --optimize float
	       iteratively estimate the fraction of aberrant cells, down to
	       the given fraction. Lowering this value from the default 1.0 to
	       say, 0.3, can help discover more events but also increases
	       noise

	   -P, --same-prob float
	       the prior probability of the query and the control sample being
	       the same. Setting to 0 calls both independently, setting to 1
	       forces the same copy number state in both.

	   -x, --xy-prob float
	       the HMM probability of transition to another copy number state.
	       Increasing this values leads to smaller and more frequent
	       calls.

   bcftools call [OPTIONS] FILE
       This command replaces the former bcftools view caller. Some of the
       original functionality has been temporarily lost in the process of
       transition under htslib, but will be added back on popular demand. The
       original calling model can be invoked with the -c option.

       File format options:
	   -o, --output FILE
	       see Common Options

	   -O, --output-type b|u|z|v
	       see Common Options

	   --ploidy ASSEMBLY[?]
	       predefined ploidy, use list (or any other unused word) to print
	       a list of all predefined assemblies. Append a question mark to
	       print the actual definition. See also --ploidy-file.

	   --ploidy-file FILE
	       ploidy definition given as a space/tab-delimited list of CHROM,
	       FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
	       correspond to the ones used by --samples-file. The default
	       ploidy can be given using the starred records (see below),
	       unlisted regions have ploidy 2. The default ploidy definition
	       is

		   X 1 60000 M 1
		   X 2699521 154931043 M 1
		   Y 1 59373566 M 1
		   Y 1 59373566 F 0
		   MT 1 16569 M 1
		   MT 1 16569 F 1
		   *  * *     M 2
		   *  * *     F 2

	   -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -R, --regions-file file
	       see Common Options

	   -s, --samples LIST
	       see Common Options

	   -S, --samples-file FILE
	       see Common Options

	   -t, --targets LIST
	       see Common Options

	   -T, --targets-file FILE
	       see Common Options

	   --threads INT
	       see Common Options

       Input/output options:
	   -A, --keep-alts
	       output all alternate alleles present in the alignments even if
	       they do not appear in any of the genotypes

	   -f, --format-fields list
	       comma-separated list of FORMAT fields to output for each
	       sample. Currently GQ and GP fields are supported. For
	       convenience, the fields can be given as lower case letters.

	   -g, --gvcf INT
	       output also gVCF blocks of homozygous REF calls. The parameter
	       INT is the minimum per-sample depth required to include a site
	       in the non-variant block.

	   -i, --insert-missed INT
	       output also sites missed by mpileup but present in -T,
	       --targets-file.

	   -M, --keep-masked-ref
	       output sites where REF allele is N

	   -V, --skip-variants snps|indels
	       skip indel/SNP sites

	   -v, --variants-only
	       output variant sites only

       Consensus/variant calling options:
	   -c, --consensus-caller
	       the original samtools/bcftools calling method (conflicts with
	       -m)

	   -C, --constrain alleles|trio

	       alleles
		   call genotypes given alleles. See also -T, --targets-file.

	       trio
		   call genotypes given the father-mother-child constraint.
		   See also -s, --samples and -n, --novel-rate.

	   -m, --multiallelic-caller
	       alternative modelfor multiallelic and rare-variant calling
	       designed to overcome known limitations in -c calling model
	       (conflicts with -c)

	   -n, --novel-rate float[,...]
	       likelihood of novel mutation for constrained -C trio calling.
	       The trio genotype calling maximizes likelihood of a particular
	       combination of genotypes for father, mother and the child
	       P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) *
	       (1-Pn). By providing three values, the mutation rate Pn is set
	       explictly for SNPs, deletions and insertions, respectively. If
	       two values are given, the first is interpreted as the mutation
	       rate of SNPs and the second is used to calculate the mutation
	       rate of indels according to their length as
	       Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for
	       insertions and a=21.9313, b=0.2856 for deletions
	       [pubmed:23975140]. If only one value is given, the same
	       mutation rate Pn is used for SNPs and indels.

	   -p, --pval-threshold float
	       with -c, accept variant if P(ref|D) < float.

	   -P, --prior float
	       expected substitution rate, or 0 to disable the prior.

	   -t, --targets file|chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -X, --chromosome-X
	       haploid output for male samples (requires PED file with -s)

	   -Y, --chromosome-Y
	       haploid output for males and skips females (requires PED file
	       with -s)

   bcftools concat [OPTIONS] FILE1 FILE2 [...]
       Concatenate or combine VCF/BCF files. All source files must have the
       same sample columns appearing in the same order. Can be used, for
       example, to concatenate chromosome VCFs into one VCF, or combine a SNP
       VCF and an indel VCF into one. The input files must be sorted by chr
       and position. The files must be given in the correct order to produce
       sorted VCF on output unless the -a, --allow-overlaps option is
       specified.

       -a, --allow-overlaps
	   First coordinate of the next file can precede last record of the
	   current file.

       -c, --compact-PS
	   Do not output PS tag at each site, only at the start of a new phase
	   set block.

       -d, --rm-dups snps|indels|both|all|none
	   Output duplicate records of specified type present in multiple
	   files only once. Requires -a, --allow-overlaps.

       -D, --remove-duplicates
	   Alias for -d none

       -f, --file-list FILE
	   Read the list of files from a file.

       -l, --ligate
	   Ligate phased VCFs by matching phase at overlapping haplotypes

       -o, --output FILE
	   see Common Options

       -O, --output-type b|u|z|v
	   see Common Options

       -q, --min-PQ INT
	   Break phase set if phasing quality is lower than INT

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options. Requires -a, --allow-overlaps.

       -R, --regions-file FILE
	   see Common Options. Requires -a, --allow-overlaps.

       --threads INT
	   see Common Options

   bcftools consensus [OPTIONS] FILE
       Create consensus sequence by applying VCF variants to a reference fasta
       file.

       -f, --fasta-ref FILE
	   reference sequence in fasta format

       -H, --haplotype 1|2
	   apply variants for the given haplotype. This option requires -s,
	   unless exactly one sample is present in the VCF

       -i, --iupac-codes
	   output variants in the form of IUPAC ambiguity codes

       -m, --mask FILE
	   BED file or TAB file with regions to be replaced with N. See
	   discussion of --regions-file in Common Options for file format
	   details.

       -o, --output FILE
	   write output to a file

       -s, --sample NAME
	   apply variants of the given sample

       Examples:

	       # Apply variants present in sample "NA001", output IUPAC codes for hets
	       bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa

	       # Create consensus for one region. The fasta header lines are then expected
	       # in the form ">chr:from-to".
	       samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz -o out.fa

   bcftools convert [OPTIONS] FILE
       VCF input options:
	   -e, --exclude EXPRESSION
	       exclude sites for which EXPRESSION is true. For valid
	       expressions see EXPRESSIONS.

	   -i, --include EXPRESSION
	       include only sites for which EXPRESSION is true. For valid
	       expressions see EXPRESSIONS.

	   -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -R, --regions-file FILE
	       see Common Options

	   -s, --samples LIST
	       see Common Options

	   -S, --samples-file FILE
	       see Common Options

	   -t, --targets LIST
	       see Common Options

	   -T, --targets-file FILE
	       see Common Options

       VCF output options:
	   -o, --output FILE
	       see Common Options

	   -O, --output-type b|u|z|v
	       see Common Options

	   --threads INT
	       see Common Options

       GEN/SAMPLE conversion:
	   -G, --gensample2vcf prefix or gen-file,sample-file
	       convert IMPUTE2 output to VCF. The second column must be of the
	       form "CHROM:POS_REF_ALT" to detect possible strand swaps;
	       IMPUTE2 leaves the first one empty ("--") when sites from
	       reference panel are filled in. See also -g below.

	   -g, --gensample prefix or gen-file,sample-file
	       convert from VCF to gen/sample format used by IMPUTE2 and
	       SHAPEIT. The columns of .gen file format are ID1,ID2,POS,A,B
	       followed by three genotype probabilities P(AA), P(AB), P(BB)
	       for each sample. In order to prevent strand swaps, the program
	       uses IDs of the form "CHROM:POS_REF_ALT". For example:

		 .gen
		 ----
		 1:111485207_G_A 1:111485207_G_A 111485207 G A 0 1 0 0 1 0
		 1:111494194_C_T 1:111494194_C_T 111494194 C T 0 1 0 0 0 1

		 .sample
		 -------
		 ID_1 ID_2 missing
		 0 0 0
		 sample1 sample1 0
		 sample2 sample2 0

	   --tag STRING
	       tag to take values for .gen file: GT,PL,GL,GP

       gVCF conversion:
	   --gvcf2vcf
	       convert gVCF to VCF, expanding REF blocks into sites. Only
	       sites with FILTER set to "PASS" or "." will be expanded.

	   -f, --fasta-ref file
	       reference sequence in fasta format. Must be indexed with
	       samtools faidx

       HAPS/SAMPLE conversion:
	   --hapsample2vcf prefix or haps-file,sample-file
	       convert from haps/sample format to VCF. The columns of .haps
	       file are similar to .gen file above, but there are only two
	       haplotype columns per sample. Note that the first column of the
	       haps file is expected to be in the form
	       "CHR:POS_REF_ALT(_END)?", with the _END being optional for
	       defining the INFO/END tag when ALT is a symbolic allele, for
	       example:

		 .haps
		 ----
		 1:111485207_G_A rsID1 111485207 G A 0 1 0 0
		 1:111494194_C_T rsID2 111494194 C T 0 1 0 0
		 1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0

	   --hapsample prefix or haps-file,sample-file
	       convert from VCF to haps/sample format used by IMPUTE2 and
	       SHAPEIT. The columns of .haps file begin with
	       ID,RSID,POS,REF,ALT. In order to prevent strand swaps, the
	       program uses IDs of the form "CHROM:POS_REF_ALT".

	   --haploid2diploid
	       with -h option converts haploid genotypes to homozygous diploid
	       genotypes. For example, the program will print 0 0 instead of
	       the default 0 -. This is useful for programs which do not
	       handle haploid genotypes correctly.

	   --vcf-ids
	       output VCF IDs instead of "CHROM:POS_REF_ALT" IDs

       HAPS/LEGEND/SAMPLE conversion:
	   -H, --haplegendsample2vcf prefix or
	   haps-file,legend-file,sample-file
	       convert from haps/legend/sample format used by IMPUTE2 to VCF,
	       see also -h, --hapslegendsample below.

	   -h, --haplegendsample prefix or haps-file,legend-file,sample-file
	       convert from VCF to haps/legend/sample format used by IMPUTE2
	       and SHAPEIT. The columns of .legend file ID,POS,REF,ALT. In
	       order to prevent strand swaps, the program uses IDs of the form
	       "CHROM:POS_REF_ALT". The .sample file is quite basic at the
	       moment with columns for population, group and sex expected to
	       be edited by the user. For example:

		 .haps
		 -----
		 0 1 0 0 1 0
		 0 1 0 0 0 1

		 .legend
		 -------
		 id position a0 a1
		 1:111485207_G_A 111485207 G A
		 1:111494194_C_T 111494194 C T

		 .sample
		 -------
		 sample population group sex
		 sample1 sample1 sample1 2
		 sample2 sample2 sample2 2

	   --haploid2diploid
	       with -h option converts haploid genotypes to homozygous diploid
	       genotypes. For example, the program will print 0 0 instead of
	       the default 0 -. This is useful for programs which do not
	       handle haploid genotypes correctly.

	   --vcf-ids
	       output VCF IDs instead of "CHROM:POS_REF_ALT" IDs

       TSV conversion:
	   --tsv2vcf file
	       convert from TSV (tab-separated values) format (such as
	       generated by 23andMe) to VCF. The input file fields can be tab-
	       or space- delimited

	   -c, --columns list
	       comma-separated list of fields in the input file. In the
	       current version, the fields CHROM, POS, ID, and AA are expected
	       and can appear in arbitrary order, columns which should be
	       ignored in the input file can be indicated by "-". The AA field
	       lists alleles on the forward reference strand, for example "CC"
	       or "CT" for diploid genotypes or "C" for haploid genotypes (sex
	       chromosomes). Insertions and deletions are not supported yet,
	       missing data can be indicated with "--".

	   -f, --fasta-ref file
	       reference sequence in fasta format. Must be indexed with
	       samtools faidx

	   -s, --samples LIST
	       list of sample names. See Common Options

	   -S, --samples-file FILE
	       file of sample names. See Common Options

	   Example:

	       # Convert 23andme results into VCF
	       bcftools convert -c ID,CHROM,POS,AA -s SampleName -f 23andme-ref.fa --tsv2vcf 23andme.txt -Oz -o out.vcf.gz

   bcftools filter [OPTIONS] FILE
       Apply fixed-threshold filters.

       -e, --exclude EXPRESSION
	   exclude sites for which EXPRESSION is true. For valid expressions
	   see EXPRESSIONS.

       -g, --SnpGap INT
	   filter SNPs within INT base pairs of an indel. The following
	   example demonstrates the logic of --SnpGap 3 applied on a deletion
	   and an insertion:

	   The SNPs at positions 1 and 7 are filtered, positions 0 and 8 are not:
		    0123456789
	       ref  .G.GT..G..
	       del  .A.G-..A..
	   Here the positions 1 and 6 are filtered, 0 and 7 are not:
		    0123-456789
	       ref  .G.G-..G..
	       ins  .A.GT..A..

       -G, --IndelGap INT
	   filter clusters of indels separated by INT or fewer base pairs
	   allowing only one to pass. The following example demonstrates the
	   logic of --IndelGap 2 applied on a deletion and an insertion:

	   The second indel is filtered:
		    012345678901
	       ref  .GT.GT..GT..
	       del  .G-.G-..G-..
	   And similarly here, the second is filtered:
		    01 23 456 78
	       ref  .A-.A-..A-..
	       ins  .AT.AT..AT..

       -i, --include EXPRESSION
	   include only sites for which EXPRESSION is true. For valid
	   expressions see EXPRESSIONS.

       -m, --mode [+x]
	   define behaviour at sites with existing FILTER annotations. The
	   default mode replaces existing filters of failed sites with a new
	   FILTER string while leaving sites which pass untouched when
	   non-empty and setting to "PASS" when the FILTER string is absent.
	   The "+" mode appends new FILTER strings of failed sites instead of
	   replacing them. The "x" mode resets filters of sites which pass to
	   "PASS". Modes "+" and "x" can both be set.

       -o, --output FILE
	   see Common Options

       -O, --output-type b|u|z|v
	   see Common Options

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       -s, --soft-filter STRING|+
	   annotate FILTER column with STRING or, with +, a unique filter name
	   generated by the program ("Filter%d").

       -S, --set-GTs .|0
	   set genotypes of failed samples to missing value (.) or reference
	   allele (0)

       -t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -T, --targets-file file
	   see Common Options

   bcftools gtcheck [OPTIONS] [-g genotypes.vcf.gz] query.vcf.gz
       Checks sample identity or, without -g, multi-sample cross-check is
       performed.

       -a, --all-sites
	   output for all sites

       -g, --genotypes genotypes.vcf.gz
	   reference genotypes to compare against

       -G, --GTs-only INT
	   use genotypes (GT) instead of genotype likelihoods (PL). When set
	   to 1, reported discordance is the number of non-matching GTs,
	   otherwise the number INT is interpreted as phred-scaled likelihood
	   of unobserved genotypes.

       -H, --homs-only
	   consider only genotypes which are homozygous in both genotypes and
	   query VCF. This may be useful with low coverage data.

       -p, --plot PREFIX
	   produce plots

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       -s, --query-sample STRING
	   query sample in query.vcf.gz. By default, the first sample is
	   checked.

       -S, --target-sample STRING
	   target sample in the -g file, used only for plotting, not for
	   analysis

       -t, --targets file
	   see Common Options

       -T, --targets-file file
	   see Common Options

       Output files format:
	   CN, Discordance
	       Pairwise discordance for all sample pairs is calculated as

		       \sum_s { min_G { PL_a(G) + PL_b(G) } },

	       where the sum runs over all sites s and G is the the most
	       likely genotype shared by both samples a and b. When PL field
	       is not present, a constant value 99 is used for the unseen
	       genotypes. With -G, the value 1 can be used instead; the
	       discordance value then gives exactly the number of differing
	       genotypes.

	   SM, Average Discordance
	       Average discordance between sample a and all other samples.

	   SM, Average Depth
	       Average depth at evaluated sites, or 1 if FORMAT/DP field is
	       not present.

	   SM, Average Number of sites
	       The average number of sites used to calculate the discordance.
	       In other words, the average number of non-missing PLs/genotypes
	       seen both samples.

   bcftools index [OPTIONS] <in.bcf>|<in.vcf.gz>
       Creates index for bgzip compressed VCF/BCF files for random access. CSI
       (coordinate-sorted index) is created by default. The CSI format
       supports indexing of chromosomes up to length 2^31. TBI (tabix index)
       index files, which support chromosome lengths up to 2^29, can be
       created by using the -t/--tbi option or using the tabix program
       packaged with htslib. When loading an index file, bcftools will try the
       CSI first and then the TBI.

       Indexing options:
	   -c, --csi
	       generate CSI-format index for VCF/BCF files [default]

	   -f, --force
	       overwrite index if it already exists

	   -m, --min-shift INT
	       set minimal interval size for CSI indices to 2^INT; default: 14

	   -t, --tbi
	       generate TBI-format index for VCF files

       Stats options:
	   -n, --nrecords
	       print the number of records based on the CSI or TBI index files

	   -s, --stats
	       Print per contig stats based on the CSI or TBI index files.
	       Output format is three tab-delimited columns listing the contig
	       name, contig length (.  if unknown) and number of records for
	       the contig. Contigs with zero records are not printed.

   bcftools isec [OPTIONS] A.vcf.gz B.vcf.gz [...]
       Creates intersections, unions and complements of VCF files. Depending
       on the options, the program can output records from one (or more) files
       which have (or do not have) corresponding records with the same
       position in the other files.

       -c, --collapse snps|indels|both|all|some|none
	   see Common Options

       -C, --complement
	   output positions present only in the first file but missing in the
	   others

       -e, --exclude -|EXPRESSION
	   exclude sites for which EXPRESSION is true. If -e (or -i) appears
	   only once, the same filtering expression will be applied to all
	   input files. Otherwise, -e or -i must be given for each input file.
	   To indicate that no filtering should be performed on a file, use
	   "-" in place of EXPRESSION, as shown in the example below. For
	   valid expressions see EXPRESSIONS.

       -f, --apply-filters LIST
	   see Common Options

       -i, --include EXPRESSION
	   include only sites for which EXPRESSION is true. See discussion of
	   -e, --exclude above.

       -n, --nfiles [+-=]INT|~BITMAP
	   output positions present in this many (=), this many or more (+),
	   this many or fewer (-), or the exact same (~) files

       -o, --output FILE
	   see Common Options. When several files are being output, their
	   names are controlled via -p instead.

       -O, --output-type b|u|z|v
	   see Common Options

       -p, --prefix DIR
	   if given, subset each of the input files accordingly. See also -w.

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       -t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -T, --targets-file file
	   see Common Options

       -w, --write LIST
	   list of input files to output given as 1-based indices. With -p and
	   no -w, all files are written.

       Examples:
	   Create intersection and complements of two sets saving the output
	   in dir/*

		   bcftools isec -p dir A.vcf.gz B.vcf.gz

	   Filter sites in A and B (but not in C) and create intersection

		   bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -p dir

	   Extract and write records from A shared by both A and B using exact
	   allele match

		   bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz

	   Extract records private to A or B comparing by position only

		   bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz

	   Print a list of records which are present in A and B but not in C
	   and D

		   bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz

   bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz [...]
       Merge multiple VCF/BCF files from non-overlapping sample sets to create
       one multi-sample file. For example, when merging file A.vcf.gz
       containing samples S1, S2 and S3 and file B.vcf.gz containing samples
       S3 and S4, the output file will contain four samples named S1, S2, S3,
       2:S3 and S4.

       Note that it is responsibility of the user to ensure that the sample
       names are unique across all files. If they are not, the program will
       exit with an error unless the option --force-samples is given. The
       sample names can be also given explicitly using the --print-header and
       --use-header options.

       Note that only records from different files can be merged, never from
       the same file. For "vertical" merge take a look at bcftools norm
       instead.

       --force-samples
	   if the merged files contain duplicate samples names, proceed
	   anyway. Duplicate sample names will be resolved by prepending index
	   of the file as it appeared on the command line to the conflicting
	   sample name (see 2:S3 in the above example).

       --print-header
	   print only merged header and exit

       --use-header FILE
	   use the VCF header in the provided text FILE

       -f, --apply-filters LIST
	   see Common Options

       -i, --info-rules -|TAG:METHOD[,...]
	   Rules for merging INFO fields (scalars or vectors) or - to disable
	   the default rules.  METHOD is one of sum, avg, min, max, join.
	   Default is DP:sum,DP4:sum if these fields exist in the input files.
	   Fields with no specified rule will take the value from the first
	   input file. The merged QUAL value is currently set to the maximum.
	   This behaviour is not user controllable at the moment.

       -l, --file-list FILE
	   read file names from FILE

       -m, --merge snps|indels|both|all|none|id
	   The option controls what types of multiallelic records can be
	   created:

	   -m none   ..	 no new multiallelics, output multiple records instead
	   -m snps   ..	 allow multiallelic SNP records
	   -m indels ..	 allow multiallelic indel records
	   -m both   ..	 both SNP and indel records can be multiallelic
	   -m all    ..	 SNP records can be merged with indel records
	   -m id     ..	 merge by ID

       -o, --output FILE
	   see Common Options

       -O, --output-type b|u|z|v
	   see Common Options

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       --threads INT
	   see Common Options

   bcftools norm [OPTIONS] file.vcf.gz
       Left-align and normalize indels, check if REF alleles match the
       reference, split multiallelic sites into multiple rows; recover
       multiallelics from multiple rows. Left-alignment and normalization will
       only be applied if the --fasta-ref option is supplied.

       -c, --check-ref e|w|x|s
	   what to do when incorrect or missing REF allele is encountered:
	   exit (e), warn (w), exclude (x), or set/fix (s) bad sites. The w
	   option can be combined with x and s. Note that s can swap alleles
	   and will update genotypes (GT) and AC counts, but will not attempt
	   to fix PL or other fields.

       -d, --rm-dup snps|indels|both|all|none
	   If a record is present in multiple files, output only the first
	   instance, see --collapse in Common Options. Requires -a,
	   --allow-overlaps.

       -D, --remove-duplicates
	   If a record is present in multiple files, output only the first
	   instance. Alias for -d none. Requires -a, --allow-overlaps.

       -f, --fasta-ref FILE
	   reference sequence. Supplying this option will turn on
	   left-alignment and normalization, however, see also the
	   --do-not-normalize option below.

       -m, --multiallelics ←|+>[snps|indels|both|any]
	   split multiallelic sites into biallelic records (-) or join
	   biallelic sites into multiallelic records (+). An optional type
	   string can follow which controls variant types which should be
	   split or merged together: If only SNP records should be split or
	   merged, specify snps; if both SNPs and indels should be merged
	   separately into two records, specify both; if SNPs and indels
	   should be merged into a single record, specify any.

       -N, --do-not-normalize
	   the -c s option can be used to fix or set the REF allele from the
	   reference -f. The -N option will not turn on indel normalisation as
	   the -f option normally implies

       -o, --output FILE
	   see Common Options

       -O, --output-type b|u|z|v
	   see Common Options

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       -s, --strict-filter
	   when merging (-m+), merged site is PASS only if all sites being
	   merged PASS

       -t, --targets LIST
	   see Common Options

       -T, --targets-file FILE
	   see Common Options

       --threads INT
	   see Common Options

       -w, --site-win INT
	   maximum distance between two records to consider when locally
	   sorting variants which changed position during the realignment

   bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]
       VCF input options:
	   -e, --exclude EXPRESSION
	       exclude sites for which EXPRESSION is true. For valid
	       expressions see EXPRESSIONS.

	   -i, --include EXPRESSION
	       include only sites for which EXPRESSION is true. For valid
	       expressions see EXPRESSIONS.

	   -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -R, --regions-file file
	       see Common Options

	   -t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -T, --targets-file file
	       see Common Options

       VCF output options:
	   -o, --output FILE
	       see Common Options

	   -O, --output-type b|u|z|v
	       see Common Options

	   --threads INT
	       see Common Options

       Plugin options:
	   -h, --help
	       list plugin’s options

	   -l, --list-plugins
	       List all available plugins.

	       By default, appropriate system directories are searched for
	       installed plugins. You can override this by setting the
	       BCFTOOLS_PLUGINS environment variable to a colon-separated list
	       of directories to search. If BCFTOOLS_PLUGINS begins with a
	       colon, ends with a colon, or contains adjacent colons, the
	       system directories are also searched at that position in the
	       list of directories.

	       If htslib is not installed systemwide, set the environment
	       variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS
	       X) to include the directory where libhts.so.1 is located.

	   -v, --verbose
	       print debugging information to debug plugin failure

	   -V, --version
	       print version string and exit

       List of plugins coming with the distribution:
	   counts
	       a minimal plugin which counts number of SNPs, Indels, and total
	       number of sites.

	   dosage
	       print genotype dosage. By default the plugin searches for PL,
	       GL and GT, in that order.

	   fill-AN-AC
	       fill INFO fields AN and AC.

	   fix-ploidy
	       sets correct ploidy

	   frameshifts
	       annotate frameshift indels

	   missing2ref
	       sets missing genotypes ("./.") to ref allele ("0/0" or "0|0")

	   tag2tag
	       Convert between similar tags, such as GL and GP.

	   vcf2sex
	       determine sample sex by checking genotypes in haploid regions

       Examples:
	       # List options common to all plugins
	       bcftools plugin

	       # List available plugins
	       bcftools plugin -l

	       # Run a plugin
	       bcftools plugin counts in.vcf

	       # Run a plugin using the abbreviated "+" notation
	       bcftools +counts in.vcf

	       # The input VCF can be streamed just like in other commands
	       cat in.vcf | bcftools +counts

	       # Print usage information of plugin "dosage"
	       bcftools +dosage -h

	       # Replace missing genotypes with 0/0
	       bcftools +missing2ref in.vcf

	       # Replace missing genotypes with 0|0
	       bcftools +missing2ref in.vcf -- -p

       Plugins troubleshooting:
	   Things to check if your plugin does not show up in the bcftools
	   plugin -l output:

	   ·   Run with the -v option for verbose output: bcftools plugin -lv

	   ·   Does the environment variable BCFTOOLS_PLUGINS include the
	       correct path?

	   ·   Are all shared libraries, namely libhts.so, accessible? Verify
	       with

	       ·   on Mac OS X: otool -L your/plugin.so and set
		   DYLD_LIBRARY_PATH if they are not

	       ·   on Linux: ldd your/plugin.so and set LD_LIBRARY_PATH if
		   they are not

	   ·   If not installed systemwide, set the environment variable
	       LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (mac) to include
	       directory where libhts.so is located.

       Plugins API:
	       // Short description used by 'bcftools plugin -l'
	       const char *about(void);

	       // Longer description used by 'bcftools +name -h'
	       const char *usage(void);

	       // Called once at startup, allows to initialize local variables.
	       // Return 1 to suppress normal VCF/BCF header output, -1 on critical
	       // errors, 0 otherwise.
	       int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);

	       // Called for each VCF record, return NULL to suppress the output
	       bcf1_t *process(bcf1_t *rec);

	       // Called after all lines have been processed to clean up
	       void destroy(void);

   bcftools polysomy [OPTIONS] file.vcf.gz
       Detect number of chromosomal copies in VCFs annotates with the
       Illumina’s B-allele frequency (BAF) values. Note that this command is
       not compiled in by default, see the section Optional Compilation with
       GSL in the INSTALL file for help.

       General options:
	   -o, --output-dir path
	       output directory

	   -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -R, --regions-file file
	       see Common Options

	   -s, --sample string
	       samply name

	   -t, --targets LIST
	       see Common Options

	   -T, --targets-file FILE
	       see Common Options

	   -v, --verbose
	       verbose debugging output which gives hints about the thresholds
	       and decisions made by the program. Note that the exact output
	       can change between versions.

       Algorithm options:
	   -b, --peak-size float
	       the minimum peak size considered as a good match can be from
	       the interval [0,1] where larger is stricter

	   -c, --cn-penalty float
	       a penalty for increasing copy number state. How this works:
	       multiple peaks are always a better fit than a single peak,
	       therefore the program prefers a single peak (normal copy
	       number) unless the absolute deviation of the multiple peaks fit
	       is significantly smaller. Here the meaning of "significant" is
	       given by the float from the interval [0,1] where larger is
	       stricter.

	   -f, --fit-th float
	       threshold for goodness of fit (normalized absolute deviation),
	       smaller is stricter

	   -i, --include-aa
	       include also the AA peak in CN2 and CN3 evaluation. This
	       usually requires increasing -f.

	   -m, --min-fraction float
	       minimum distinguishable fraction of aberrant cells. The
	       experience shows that trustworthy are estimates of 20% and
	       more.

	   -p, --peak-symmetry float
	       a heuristics to filter failed fits where the expected peak
	       symmetry is violated. The float is from the interval [0,1] and
	       larger is stricter

   bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz [...]]
       Extracts fields from VCF or BCF files and outputs them in user-defined
       format.

       -c, --collapse snps|indels|both|all|some|none
	   see Common Options

       -e, --exclude EXPRESSION
	   exclude sites for which EXPRESSION is true. For valid expressions
	   see EXPRESSIONS.

       -f, --format FORMAT
	   learn by example, see below

       -H, --print-header
	   print header

       -i, --include EXPRESSION
	   include only sites for which EXPRESSION is true. For valid
	   expressions see EXPRESSIONS.

       -l, --list-samples
	   list sample names and exit

       -o, --output FILE
	   see Common Options

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       -s, --samples LIST
	   see Common Options

       -S, --samples-file FILE
	   see Common Options

       -t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -T, --targets-file file
	   see Common Options

       -u, --allow-undef-tags
	   do not throw an error if there are undefined tags in the format
	   string, print "." instead

       -v, --vcf-list FILE
	   process multiple VCFs listed in the file

       Format:
	       %CHROM	       The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
	       %INFO/TAG       Any tag in the INFO column
	       %TYPE	       Variant type (REF, SNP, MNP, INDEL, OTHER)
	       %MASK	       Indicates presence of the site in other files (with multiple files)
	       %TAG{INT}       Curly brackets to subscript vectors (0-based)
	       %FIRST_ALT      Alias for %ALT{0}
	       []	       The brackets loop over all samples
	       %GT	       Genotype (e.g. 0/1)
	       %TGT	       Translated genotype (e.g. C/A)
	       %IUPACGT	       Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
	       %LINE	       Prints the whole line
	       %SAMPLE	       Sample name

       Examples:
	       bcftools query -f '%CHROM  %POS	%REF  %ALT{0}\n' file.vcf.gz
	       bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

   bcftools reheader [OPTIONS] file.vcf.gz
       Modify header of VCF/BCF files, change sample names.

       -h, --header FILE
	   new VCF header

       -o, --output FILE
	   see Common Options

       -s, --samples FILE
	   new sample names, one name per line, in the same order as they
	   appear in the VCF file. Alternatively, only samples which need to
	   be renamed can be listed as "old_name new_name\n" pairs separated
	   by whitespaces, each on separate line.

   bcftools roh [OPTIONS] file.vcf.gz
       A program for detecting runs of homo/autozygosity. Only bi-allelic
       sites are considered.

       The HMM model:
	       Notation:
		 D  = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity),
		 f  = non-ref allele frequency

	       Emission probabilities:
		 oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA)
		 oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA)

	       Transition probabilities:
		 tAZ = P(AZ|HW)	 .. from HW to AZ, the -a parameter
		 tHW = P(HW|AZ)	 .. from AZ to HW, the -H parameter

		 ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
		 AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
		 HWi = P_i(HW)

		 P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
		 P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]

       General Options:
	   --AF-dflt FLOAT
	       in case allele frequency is not known, use the FLOAT. By
	       default, sites where allele frequency cannot be determined, or
	       is 0, are skipped.

	   --AF-tag TAG
	       use the specified INFO tag TAG as an allele frequency estimate
	       instead of the defaul AC and AN tags. Sites which do not have
	       TAG will be skipped.

	   --AF-file FILE
	       Read allele frequencies from a tab-delimited file containing
	       the columns: CHROM\tPOS\tREF,ALT\tAF. The file can be
	       compressed with bgzip and indexed with tabix -s1 -b2 -e2. Sites
	       which are not present in the FILE or have different reference
	       or alternate allele will be skipped. Note that such a file can
	       be easily created from a VCF using:

		   bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/TAG\n' file.vcf | bgzip -c > freqs.tab.gz

	   -e, --estimate-AF FILE
	       recalculate INFO/AC and INFO/AN on the fly, using either all
	       samples ("-") or samples listed in FILE. By default, allele
	       frequency is estimated from AC and AN counts which are already
	       present in the INFO field.

	   -G, --GTs-only FLOAT
	       use genotypes (FORMAT/GT fields) ignoring genotype likelihoods
	       (FORMAT/PL), setting PL of unseen genotypes to FLOAT. Safe
	       value to use is 30 to account for GT errors.

	   -I, --skip-indels
	       skip indels as their genotypes are usually enriched for errors

	   -m, --genetic-map FILE
	       genetic map in the format required also by IMPUTE2. Only the
	       first and third column are used (position and Genetic_Map(cM)).
	       The FILE can chromosome name.

	   -M, --rec-rate FLOAT
	       constant recombination rate per bp

	   -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -R, --regions-file file
	       see Common Options

	   -s, --sample name
	       the name of sample to analyze

	   -t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -T, --targets-file file
	       see Common Options

       HMM Options:
	   -a, --hw-to-az FLOAT
	       P(AZ|HW) transition probability from AZ (autozygous) to HW
	       (Hardy-Weinberg) state

	   -H, --az-to-hw FLOAT
	       P(HW|AZ) transition probability from HW to AZ state

	   -V, --viterbi-training
	       perform Viterbi training to estimate transition probabilities

   bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]
       Parses VCF or BCF and produces text file stats which is suitable for
       machine processing and can be plotted using plot-vcfstats. When two
       files are given, the program generates separate stats for intersection
       and the complements. By default only sites are compared, -s/-S must
       given to include also sample columns.

       -1, --1st-allele-only
	   consider only the 1st alternate allele at multiallelic sites

       -c, --collapse snps|indels|both|all|some|none
	   see Common Options

       -d, --depth INT,INT,INT
	   ranges of depth distribution: min, max, and size of the bin

       --debug
	   produce verbose per-site and per-sample output

       -e, --exclude EXPRESSION
	   exclude sites for which EXPRESSION is true. For valid expressions
	   see EXPRESSIONS.

       -E, --exons file.gz
	   tab-delimited file with exons for indel frameshifts statistics. The
	   columns of the file are CHR, FROM, TO, with 1-based, inclusive,
	   positions. The file is BGZF-compressed and indexed with tabix

	       tabix -s1 -b2 -e3 file.gz

       -f, --apply-filters LIST
	   see Common Options

       -F, --fasta-ref ref.fa
	   faidx indexed reference sequence file to determine INDEL context

       -i, --include EXPRESSION
	   include only sites for which EXPRESSION is true. For valid
	   expressions see EXPRESSIONS.

       -I, --split-by-ID
	   collect stats separately for sites which have the ID column set
	   ("known sites") or which do not have the ID column set ("novel
	   sites").

       -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -R, --regions-file file
	   see Common Options

       -s, --samples LIST
	   see Common Options

       -S, --samples-file FILE
	   see Common Options

       -t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
	   see Common Options

       -T, --targets-file file
	   see Common Options

       -u, --user-tstv <TAG[:min:max:n]>
	   collect Ts/Tv stats for any tag using the given binning [0:1:100]

       -v, --verbose
	   produce verbose per-site and per-sample output

   bcftools view [OPTIONS] file.vcf.gz [REGION [...]]
       View, subset and filter VCF or BCF files by position and filtering
       expression. Convert between VCF and BCF. Former bcftools subset.

       Output options
	   -G, --drop-genotypes
	       drop individual genotype information (after subsetting if -s
	       option is set)

	   -h, --header-only
	       output the VCF header only

	   -H, --no-header
	       suppress the header in VCF output

	   -l, --compression-level [0-9]
	       compression level. 0 stands for uncompressed, 1 for best speed
	       and 9 for best compression.

	   -O, --output-type b|u|z|v
	       see Common Options

	   -o, --output-file FILE: output file name. If not present, the
	   default is to print to standard output (stdout).

	   -r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -R, --regions-file file
	       see Common Options

	   -t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
	       see Common Options

	   -T, --targets-file file
	       see Common Options

	   --threads INT
	       see Common Options

       Subset options:
	   -a, --trim-alt-alleles
	       trim alternate alleles not seen in subset. Type A, G and R INFO
	       and FORMAT fields will also be trimmed

	   --force-samples
	       only warn about unknown subset samples

	   -I, --no-update
	       do not (re)calculate INFO fields for the subset (currently
	       INFO/AC and INFO/AN)

	   -s, --samples LIST
	       see Common Options

	   -S, --samples-file FILE
	       see Common Options

       Filter options:
	   -c, --min-ac INT[:nref|:alt1|:minor|:major|:'nonmajor']
	       minimum allele count (INFO/AC) of sites to be printed.
	       Specifying the type of allele is optional and can be set to
	       non-reference (nref, the default), 1st alternate (alt1), the
	       least frequent (minor), the most frequent (major) or sum of all
	       but the most frequent (nonmajor) alleles.

	   -C, --max-ac INT[:nref|:alt1|:minor|:'major'|:'nonmajor']
	       maximum allele count (INFO/AC) of sites to be printed.
	       Specifying the type of allele is optional and can be set to
	       non-reference (nref, the default), 1st alternate (alt1), the
	       least frequent (minor), the most frequent (major) or sum of all
	       but the most frequent (nonmajor) alleles.

	   -e, --exclude EXPRESSION
	       exclude sites for which EXPRESSION is true. For valid
	       expressions see EXPRESSIONS.

	   -f, --apply-filters LIST
	       see Common Options

	   -g, --genotype [^][hom|het|miss]
	       include only sites with one or more homozygous (hom),
	       heterozygous (het) or missing (miss) genotypes. When prefixed
	       with ^, the logic is reversed; thus ^het excludes sites with
	       heterozygous genotypes.

	   -i, --include EXPRESSION
	       include sites for which EXPRESSION is true. For valid
	       expressions see EXPRESSIONS.

	   -k, --known
	       print known sites only (ID column is not ".")

	   -m, --min-alleles INT
	       print sites with at least INT alleles listed in REF and ALT
	       columns

	   -M, --max-alleles INT
	       print sites with at most INT alleles listed in REF and ALT
	       columns. Use -m2 -M2 -v snps to only view biallelic SNPs.

	   -n, --novel
	       print novel sites only (ID column is ".")

	   -p, --phased
	       print sites where all samples are phased. Haploid genotypes are
	       considered phased. Missing genotypes considered unphased unless
	       the phased bit is set.

	   -P, --exclude-phased
	       exclude sites where all samples are phased

	   -q, --min-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
	       minimum allele frequency (INFO/AC / INFO/AN) of sites to be
	       printed. Specifying the type of allele is optional and can be
	       set to non-reference (nref, the default), 1st alternate (alt1),
	       the least frequent (minor), the most frequent (major) or sum of
	       all but the most frequent (nonmajor) alleles.

	   -Q, --max-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
	       maximum allele frequency (INFO/AC / INFO/AN) of sites to be
	       printed. Specifying the type of allele is optional and can be
	       set to non-reference (nref, the default), 1st alternate (alt1),
	       the least frequent (minor), the most frequent (major) or sum of
	       all but the most frequent (nonmajor) alleles.

	   -u, --uncalled
	       print sites without a called genotype

	   -U, --exclude-uncalled
	       exclude sites without a called genotype

	   -v, --types snps|indels|mnps|other
	       comma-separated list of variant types to select. Site is
	       selected if any of the ALT alleles is of the type requested.
	       Types are determined by comparing the REF and ALT alleles in
	       the VCF record not INFO tags like INFO/INDEL or INFO/VT. Use
	       --include to select based on INFO tags.

	   -V, --exclude-types snps|indels|mnps|other
	       comma-separated list of variant types to exclude. Site is
	       excluded if any of the ALT alleles is of the type requested.
	       Types are determined by comparing the REF and ALT alleles in
	       the VCF record not INFO tags like INFO/INDEL or INFO/VT. Use
	       --exclude to exclude based on INFO tags.

	   -x, --private
	       print sites where only the subset samples carry an
	       non-reference allele. Requires --samples or --samples-file.

	   -X, --exclude-private
	       exclude sites where only the subset samples carry an
	       non-reference allele

   bcftools help [COMMAND] | bcftools --help [COMMAND]
       Display a brief usage message listing the bcftools commands available.
       If the name of a command is also given, e.g., bcftools help view, the
       detailed usage message for that particular command is displayed.

   bcftools [--version|-v]
       Display the version numbers and copyright information for bcftools and
       the important libraries used by bcftools.

   bcftools [--version-only]
       Display the full bcftools version number in a machine-readable format.

EXPRESSIONS
       These filtering expressions are accepted by annotate, filter, query and
       view commands.

       Valid expressions may contain:

       ·   numerical constants, string constants, file names

	       1, 1.0, 1e-4
	       "String"
	       @file_name

       ·   arithmetic operators

	       +,*,-,/

       ·   comparison operators

	       == (same as =), >, >=, <=, <, !=

       ·   regex operators "~" and its negation "!~"

	       INFO/HAYSTACK ~ "needle"

       ·   parentheses

	       (, )

       ·   logical operators

	       && (same as &), ||,  |

       ·   INFO tags, FORMAT tags, column names

	       INFO/DP or DP
	       FORMAT/DV, FMT/DV, or DV
	       FILTER, QUAL, ID, POS, REF, ALT[0]

       ·   1 (or 0) to test the presence (or absence) of a flag

	       FlagA=1 && FlagB=0

       ·   "." to test missing values

	       DP=".", DP!=".", ALT="."

       ·   missing genotypes can be matched regardless of phase and ploidy
	   (".|.", "./.", ".") using this expression

	       GT="."

       ·   TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)

	       TYPE="indel" | TYPE="snp"

       ·   array subscripts, "*" for any field

	       (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
	       DP4[*] == 0
	       CSQ[*] ~ "missense_variant.*deleterious"

       ·   function on FORMAT tags (over samples) and INFO tags (over vector
	   fields)

	       MAX, MIN, AVG, SUM, STRLEN, ABS

       ·   variables calculated on the fly if not present: number of alternate
	   alleles; number of samples; count of alternate alleles; minor
	   allele count (similar to AC but is always smaller than 0.5);
	   frequency of alternate alleles (AF=AC/AN); frequency of minor
	   alleles (MAF=MAC/AN); number of alleles in called genotypes

	       N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN

       Notes:

       ·   String comparisons and regular expressions are case-insensitive

       ·   If the subscript "*" is used in regular expression search, the
	   whole field is treated as one string. For example, the regex
	   STR[*]~"B,C" will be true for the string vector INFO/STR=AB,CD.

       ·   Variables and function names are case-insensitive, but not tag
	   names. For example, "qual" can be used instead of "QUAL",
	   "strlen()" instead of "STRLEN()" , but not "dp" instead of "DP".

       Examples:

	   MIN(DV)>5

	   MIN(DV/DP)>0.3

	   MIN(DP)>10 & MIN(DV)>3

	   FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample

	   FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples

	   QUAL>10 |  FMT/GQ>10	  .. selects only GQ>10 samples

	   QUAL>10 || FMT/GQ>10	  .. selects all samples at QUAL>10 sites

	   TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)

	   MIN(DP)>35 && AVG(GQ)>50

	   ID=@file	  .. selects lines with ID present in the file

	   ID!=@~/file	  .. skip lines with ID present in the ~/file

	   MAF[0]<0.05	  .. select rare variants at 5% cutoff

	   POS>=100   .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.

       Shell expansion:

       Note that expressions must often be quoted because some characters have
       special meaning in the shell. An example of expression enclosed in
       single quotes which cause that the whole expression is passed to the
       program as intended:

	   bcftools view -i '%ID!="." & MAF[0]<0.01'

       Please refer to the documentation of your shell for details.

SCRIPTS AND OPTIONS
   plot-vcfstats [OPTIONS] file.vchk [...]
       Script for processing output of bcftools stats. It can merge results
       from multiple outputs (useful when running the stats for each
       chromosome separately), plots graphs and creates a PDF presentation.

       -m, --merge
	   Merge vcfstats files to STDOUT, skip plotting.

       -p, --prefix PATH
	   The output files prefix, add a slash to create new directory.

       -P, --no-PDF
	   Skip the PDF creation step.

       -r, --rasterize
	   Rasterize PDF images for faster rendering.

       -s, --sample-names
	   Use sample names for xticks rather than numeric IDs.

       -t, --title STRING
	   Identify files by these titles in plots. The option can be given
	   multiple times, for each ID in the bcftools stats output. If not
	   present, the script will use abbreviated source file names for the
	   titles.

       -T, --main-title STRING
	   Main title for the PDF.

PERFORMANCE
       HTSlib was designed with BCF format in mind. When parsing VCF files,
       all records are internally converted into BCF representation. Simple
       operations, like removing a single column from a VCF file, can be
       therefore done much faster with standard UNIX commands, such as awk or
       cut. Therefore it is recommended to use BCF as input/output format
       whenever possible to avoid large overhead of the VCF → BCF → VCF
       conversion.

BUGS
       Please report any bugs you encounter on the github website:
       http://github.com/samtools/bcftools

AUTHORS
       Heng Li from the Sanger Institute wrote the original C version of
       htslib, samtools and bcftools. Bob Handsaker from the Broad Institute
       implemented the BGZF library. Petr Danecek, Shane McCarthy and John
       Marshall are maintaining and further developing bcftools. Many other
       people contributed to the program and to the file format
       specifications, both directly and indirectly by providing patches,
       testing and reporting bugs. We thank them all.

RESOURCES
       BCFtools GitHub website: http://github.com/samtools/bcftools

       Samtools GitHub website: http://github.com/samtools/samtools

       HTSlib GitHub website: http://github.com/samtools/htslib

       File format specifications: http://samtools.github.io/hts-specs

       BCFtools documentation: http://samtools.github.io/bcftools

       BCFtools wiki page: https://github.com/samtools/bcftools/wiki

COPYING
       The MIT/Expat License or GPL License, see the LICENSE document for
       details. Copyright (c) Genome Research Ltd.

			     2015-12-15 14:02 GMT		   BCFTOOLS(1)
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