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Missing DP field in Haplotype Caller produced vcf file
Hi, so I have some data that I ran through both Unified Genotype AND Haplotype Caller (because I wanted to see the difference in the number and quality of SNPs returned). I have merged both vcf files (using a simple awk command) to produce one that contains concordant SNPs between the two. However, I am now about to filter on GQ and DP except that I don't have a DP field in the file containing the SNPs that both programs called. Neither does it appear in the Haplotype Caller file. It DOES appear in the Unified Genotyper file though. I really would like to continue using my concordant file: is there a way that I can force the addition of the DP field into the Haplotype Caller vcf? I have the AD field showing the read numbers for both alleles, and the DP field is included in the INFO column but I can't filter depth at present so I'd really appreciate some guidance with this. PS. I'm a newbie to bioinformatics processing and computing. Thanks for any help given.