.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 .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)