Meaning Of -A In Vcftools Vcfutils.Pl Varfilter?

Question

[Dan]

The command line says:

Usage:   vcfutils.pl varFilter [options] <in.vcf>

Options: -Q INT    minimum RMS mapping quality for SNPs [10]
         -d INT    minimum read depth [2]
         -D INT    maximum read depth [10000000]
         -a INT    minimum number of alternate bases [2]
         -w INT    SNP within INT bp around a gap to be filtered [3]
         -W INT    window size for filtering adjacent gaps [10]
         -1 FLOAT  min P-value for strand bias (given PV4) [0.0001]
         -2 FLOAT  min P-value for baseQ bias [1e-100]
         -3 FLOAT  min P-value for mapQ bias [0]
         -4 FLOAT  min P-value for end distance bias [0.0001]
         -e FLOAT  min P-value for HWE (plus F<0) [0.0001]
         -p        print filtered variants

Note: Some of the filters rely on annotations generated by SAMtools/BCFtools.

The description of -a seems counter intuitive, why would you want two alternative alleles as the default?

Is this better written "minimum number of alternate reads supporting each alternative allele [2]"?

That would at least make sense as an option to have.

P.S. anyone know which filters rely on annotations generated by SAMtools/BCFtools?

[Dan]

Anyone know why -p is an option ;-)

Answer 1

[pd3]

The help message wording may be confusing, it should read, as you suggested, the "minimum number of alternate reads supporting the alternative allele".

The most useful annotations in v0.1.19 are RPB, MDV, QBD, QUAL and SnpGap from vcftools. The exact combination of annotations depends on the data, a bit of experimentation is needed.