tested version for tbam2gbam

[rsem.git] / sam / bcftools / bcftools.1

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-.TH bcftools 1 "2 October 2010" "bcftools" "Bioinformatics tools"
-.SH NAME
-.PP
-bcftools - Utilities for the Binary Call Format (BCF) and VCF.
-.SH SYNOPSIS
-.PP
-bcftools index in.bcf
-.PP
-bcftools view in.bcf chr2:100-200 > out.vcf
-.PP
-bcftools view -vc in.bcf > out.vcf 2> out.afs
-
-.SH DESCRIPTION
-.PP
-Bcftools is a toolkit for processing VCF/BCF files, calling variants and
-estimating site allele frequencies and allele frequency spectrums.
-
-.SH COMMANDS AND OPTIONS
-
-.TP 10
-.B view
-.B bcftools view
-.RB [ \-cbuSAGgHvNQ ]
-.RB [ \-1
-.IR nGroup1 ]
-.RB [ \-l
-.IR listFile ]
-.RB [ \-t
-.IR mutRate ]
-.RB [ \-p
-.IR varThres ]
-.RB [ \-P
-.IR prior ]
-.I in.bcf
-.RI [ region ]
-
-Convert between BCF and VCF, call variant candidates and estimate allele
-frequencies.
-
-.B OPTIONS:
-.RS
-.TP 10
-.B -b
-Output in the BCF format. The default is VCF.
-.TP
-.B -c
-Call variants.
-.TP
-.B -v
-Output variant sites only (force -c)
-.TP
-.B -g
-Call per-sample genotypes at variant sites (force -c)
-.TP
-.B -u
-Uncompressed BCF output (force -b).
-.TP
-.B -S
-The input is VCF instead of BCF.
-.TP
-.B -A
-Retain all possible alternate alleles at variant sites. By default, this
-command discards unlikely alleles.
-.TP
-.B -G
-Suppress all individual genotype information.
-.TP
-.B -H
-Perform Hardy-Weiberg Equilibrium test. This will add computation time, sometimes considerably.
-.TP
-.B -N
-Skip sites where the REF field is not A/C/G/T
-.TP
-.B -Q
-Output the QCALL likelihood format
-.TP
-.B -f
-Reference-free variant calling mode. In this mode, the prior will be
-folded; a variant is called iff the sample(s) contains at least two
-alleles; the QUAL field in the VCF/BCF output is changed accordingly.
-.TP
-.BI "-1 " INT
-Number of group-1 samples. This option is used for dividing input into
-two groups for comparing. A zero value disables this functionality. [0]
-.TP
-.BI "-l " FILE
-List of sites at which information are outputted [all sites]
-.TP
-.BI "-t " FLOAT
-Scaled muttion rate for variant calling [0.001]
-.TP
-.BI "-p " FLOAT
-A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
-.TP
-.BI "-P " STR
-Prior or initial allele frequency spectrum. If STR can be
-.IR full ,
-.IR cond2 ,
-.I flat
-or the file consisting of error output from a previous variant calling
-run.
-.RE
-
-.TP
-.B index
-.B bcftools index
-.I in.bcf
-
-Index sorted BCF for random access.
-.RE
-
-.TP
-.B cat
-.B bcftools cat
-.I in1.bcf
-.RI [ "in2.bcf " [ ... "]]]"
-
-Concatenate BCF files. The input files are required to be sorted and
-have identical samples appearing in the same order.
-.RE