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?