I have a vcf output from Annovar (and wAnnovar), and need some help understanding all of the headers. I know i am given the reference and the alternative allele. However, I want to know how many reads in my input file were reference and alternative.
I'm looking at the vcf file, and see some trailing information. What do these mean? Do these value tell me how many reads per allele?
ADP=5;WT=0;HET=1;HOM=0;NC=0
GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:6:5:5:3:2:40%:2.2222E-1:75:48:3:0:2:0