1 .TH bcftools 1 "2 October 2010" "bcftools" "Bioinformatics tools"
4 bcftools - Utilities for the Binary Call Format (BCF) and VCF.
9 bcftools view in.bcf chr2:100-200 > out.vcf
11 bcftools view -vc in.bcf > out.vcf 2> out.afs
15 Bcftools is a toolkit for processing VCF/BCF files, calling variants and
16 estimating site allele frequencies and allele frequency spectrums.
18 .SH COMMANDS AND OPTIONS
37 Convert between BCF and VCF, call variant candidates and estimate allele
44 Output in the BCF format. The default is VCF.
50 Output variant sites only (force -c)
53 Call per-sample genotypes at variant sites (force -c)
56 Uncompressed BCF output (force -b).
59 The input is VCF instead of BCF.
62 Retain all possible alternate alleles at variant sites. By default, this
63 command discards unlikely alleles.
66 Suppress all individual genotype information.
69 Perform Hardy-Weiberg Equilibrium test. This will add computation time, sometimes considerably.
72 Skip sites where the REF field is not A/C/G/T
75 Output the QCALL likelihood format
78 Reference-free variant calling mode. In this mode, the prior will be
79 folded; a variant is called iff the sample(s) contains at least two
80 alleles; the QUAL field in the VCF/BCF output is changed accordingly.
83 Number of group-1 samples. This option is used for dividing input into
84 two groups for comparing. A zero value disables this functionality. [0]
87 List of sites at which information are outputted [all sites]
90 Scaled muttion rate for variant calling [0.001]
93 A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
96 Prior or initial allele frequency spectrum. If STR can be
100 or the file consisting of error output from a previous variant calling
109 Index sorted BCF for random access.
116 .RI [ "in2.bcf " [ ... "]]]"
118 Concatenate BCF files. The input files are required to be sorted and
119 have identical samples appearing in the same order.