I want to use vcf-merge or vcf-intersect on multiple vcf files and then filter the variants based on their quality and DP values. I have a basic question regarding the way vcftools work !
When i intersect two or more vcf files, the QUAL and DP values of a varant in the 1st vcf file is always being shown in the resulted vcf file. The QUAL/DP values of remaining vcf files are being ignored !! If it is the case then filtering after intersection is difficult.
When i merge 2 vcf files i am getting 2 different collumns for different genotypes, which is completely fine but why the average QUAL vales and sum of DP values are being shown ? For example 1st vcf file has a SNP with QUAL=40 and DP=2 and 2nd vcf file has the same SNP with QUAL=200 and DP=50 then the merged vcf file will have the variant with QUAL=120 and DP=52, which is quite promission even though the variant quality and DP were bad in 1 vcf file. In this case also the filtering after merging is difficult.
should i filter the variant before merging them ? Any suggestions will be highly appreciated.