I am using samtools mpileup for SNP calling, then with BEAGLE I do the haplotyping and with GATK BeagleOutputToVCF I convert the beagle output back to vcf format. Everything is working fine, but I miss one tag.
I want to add the DP tag to the genotype field of the vcf file. Is there an option in samtools mpileup, BEAGLE or GATK BeagleOutputToVCF which can add this information? Do I have to use the tool mentioned in incorporating raw read coverage per sample in merged vcf which requires much IO for calculation and is an extra step in my pipeline? Or is this information somewhere in my vcf file? My vcf file looks like this:
SL2.40ch12 17 . T C 69.50 . AC=1;AC1=1;AF=0.167;AF1=0.1766;AN=6;DP=39;DP4=10,7,2,3;FQ=70.3;MQ=46;NumGenotypesChanged=0;PV4=0.62,0.24,0.034,1;R2=0.922;RPB=5.484225e-01;VDB=3.008871e-02 GT:GQ:OG:PL 0|0:13:.:0,9,90 0|0:60:.:0,39,255 0|1:21:.:104,0,11