I was wondering how to filter the vcf file based on a few input arguments ( DP>10, MQ>30 and QD>20 or GT = "1/1" etc)? I m planning to use simple command on the command line to extract the info and create a new filtered vcf file. I want to keep the 20 lines of vcf header INFO in new file as well. I can do it with perl but is there any other easy way? Last time I extracted my required info from vcf file using vcftools but I couldnt get a filtered vcf file.
My command
vcftools --vcf GMM_homo.vcf --depth --FILTER-summary --TsTv-by-count --site-mean-depth --SNPdensity 1000 --site-pi --minQ 30 --min-meanDP 5 --out homo_GMM