Hello all,
I'm encountering a surprising problem while filtering a vcf file in bcftools (v1.1-52-ga2e5b56). It doesn't look like a proper bug but leaves be bewildered enough.
I'm trying to filter out all variant sites, and retain only fixed sites. So, logically enough, I apply a filter to discard sites where minor allele count is above zero, with :
bcftools view --max-ac 0:minor
It mostly works, but only mostly : at some sites, the odd heterozygous individual is retained (0/1:2,1:3:30:30,0,65 for ex in a mostly 0/0 line). This is not a problem of a deadlock between two alleles with equal frequency (thus no minor), since this odd "1" is the only one with 100+ "0"s.
So, I believe there must be some kind of hidden tolerance threshold somewhere, but, does any one have a workaround..?
Thanks a lot for insight !
Robin
I'm encountering a surprising problem while filtering a vcf file in bcftools (v1.1-52-ga2e5b56). It doesn't look like a proper bug but leaves be bewildered enough.
I'm trying to filter out all variant sites, and retain only fixed sites. So, logically enough, I apply a filter to discard sites where minor allele count is above zero, with :
bcftools view --max-ac 0:minor
It mostly works, but only mostly : at some sites, the odd heterozygous individual is retained (0/1:2,1:3:30:30,0,65 for ex in a mostly 0/0 line). This is not a problem of a deadlock between two alleles with equal frequency (thus no minor), since this odd "1" is the only one with 100+ "0"s.
So, I believe there must be some kind of hidden tolerance threshold somewhere, but, does any one have a workaround..?
Thanks a lot for insight !
Robin
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