I'm wondering if anyone knows how to filter heterozygous genotype calls from a vcf file where, for either allele, there is only one read supporting the call. So the allelic depth would be n,1 or 1,n. n meaning the depth could be anything. I'm thinking that we are getting a lot of wrong heterozygous calls due to sequencing error. I tried vcffilter using the command:
vcffilter -g "! ( GT = 0/1 & AD = 1,* OR AD = *,1 )"
Any one else have any thoughts?