bcftools view options

Question

[897598644]

Excuse me:

In the command of bcftools view -bvcg, what does the option -b mean?

Thanks in advance!

Answer 1

[Steven Lakin]

The -b flag will cause it to output BCF (Binary VCF) instead of a VCF (Variant Call Format) file.

The online documentation didn't include that flag, but the command-line documentation has it:

Usage: bcftools view [options] <in.bcf> [reg]

Input/output options:

       -A        keep all possible alternate alleles at variant sites
       -b        output BCF instead of VCF
       -D FILE   sequence dictionary for VCF->BCF conversion [null]
       -F        PL generated by r921 or before (which generate old ordering)
       -G        suppress all individual genotype information
       -l FILE   list of sites (chr pos) or regions (BED) to output [all sites]
       -L        calculate LD for adjacent sites
       -N        skip sites where REF is not A/C/G/T
       -Q        output the QCALL likelihood format
       -s FILE   list of samples to use [all samples]
       -S        input is VCF
       -u        uncompressed BCF output (force -b)

Consensus/variant calling options:

       -c        SNP calling (force -e)
       -d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]
       -e        likelihood based analyses
       -g        call genotypes at variant sites (force -c)
       -i FLOAT  indel-to-substitution ratio [-1]
       -I        skip indels
       -m FLOAT  alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT
       -p FLOAT  variant if P(ref|D)<FLOAT [0.5]
       -P STR    type of prior: full, cond2, flat [full]
       -t FLOAT  scaled substitution mutation rate [0.001]
       -T STR    constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]
       -v        output potential variant sites only (force -c)

Contrast calling and association test options:

       -1 INT    number of group-1 samples [0]
       -C FLOAT  posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [1]
       -U INT    number of permutations for association testing (effective with -1) [0]
       -X FLOAT  only perform permutations for P(chi^2)<FLOAT [0.01]