bcftools(1)                  Bioinformatics tools                  bcftools(1)



NAME
       bcftools - Utilities for the Binary Call Format (BCF) and VCF.

SYNOPSIS
       bcftools index in.bcf

       bcftools view in.bcf chr2:100-200 > out.vcf

       bcftools view -vc in.bcf > out.vcf 2> out.afs


DESCRIPTION
       Bcftools  is  a  toolkit for processing VCF/BCF files, calling variants
       and estimating site allele frequencies and allele frequency  spectrums.


COMMANDS AND OPTIONS
       view      bcftools  view  [-cbuSAGgHvNQ] [-1 nGroup1] [-l listFile] [-t
                 mutRate] [-p varThres] [-P prior] in.bcf [region]

                 Convert between BCF and  VCF,  call  variant  candidates  and
                 estimate allele frequencies.

                 OPTIONS:

                 -b        Output in the BCF format. The default is VCF.

                 -c        Call variants.

                 -v        Output variant sites only (force -c)

                 -g        Call  per-sample  genotypes at variant sites (force
                           -c)

                 -u        Uncompressed BCF output (force -b).

                 -S        The input is VCF instead of BCF.

                 -A        Retain all possible alternate  alleles  at  variant
                           sites.  By  default, this command discards unlikely
                           alleles.

                 -G        Suppress all individual genotype information.

                 -H        Perform Hardy-Weiberg Equilibrium test.  This  will
                           add computation time, sometimes considerably.

                 -N        Skip sites where the REF field is not A/C/G/T

                 -Q        Output the QCALL likelihood format

                 -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 accord-
                           ingly.

                 -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]

                 -l FILE   List  of  sites  at which information are outputted
                           [all sites]

                 -t FLOAT  Scaled muttion rate for variant calling [0.001]

                 -p FLOAT  A  site  is  considered  to   be   a   variant   if
                           P(ref|D)<FLOAT [0.5]

                 -P STR    Prior  or initial allele frequency spectrum. If STR
                           can be full, cond2, flat or the file consisting  of
                           error output from a previous variant calling run.


       index     bcftools index in.bcf

                 Index sorted BCF for random access.


       cat       bcftools cat in1.bcf [in2.bcf [...]]]

                 Concatenate  BCF  files.  The  input files are required to be
                 sorted and have  identical  samples  appearing  in  the  same
                 order.



bcftools                        2 October 2010                     bcftools(1)
