I would like filter the vcf file using DP and GQ thresholds at sites where atleast 80% of the individuals meeting the thresholds. More precisely, i have the below two scenarios:
Retain sites where atleast 80% of the individuals had at least depth DP >= 10 and GQ>=20 irrespective of the reference or non-reference allele.
Retain sites where atleast one sample has the non-reference allele with DP>= 10 and GQ >= 20.
I checked the vcftools documentation but could not find where i could specify the minimum number of individuals. I believe there could an existing thread or solution to acheive this. Could someone refer the solution here.