The command line says:
Usage: vcfutils.pl varFilter [options] <in.vcf> Options: -Q INT minimum RMS mapping quality for SNPs  -d INT minimum read depth  -D INT maximum read depth  -a INT minimum number of alternate bases  -w INT SNP within INT bp around a gap to be filtered  -W INT window size for filtering adjacent gaps  -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  -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 "?
That would at least make sense as an option to have.
P.S. anyone know which filters rely on annotations generated by SAMtools/BCFtools?