let me start by saying I've spent hours at the http://vcftools.sourceforge.net/specs.html but I still don't understand some of the vcf fields.
For example, In the following record I dont understand some of the GT:AD:DP:GQ:PL information
chr1 897723 rs6696911 C T 453.42 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-0.479;DB;DP=36;Dels=0.00;FS=1.480;HRun=2;HaplotypeScore=0.0000;MQ=41.37;MQ0=0;MQRankSum=-0.578;QD=12.60;ReadPosRankSum=0.842
GT=1/1 I'm pretty sure both allele have T's. Whereas 1/0 would mean hetro for ref and snp? AD = 19,17 - I cant find and explanation what AD means? DP = 36 easy to understand GQ = 87.16 Why are there two values in this field? PL = 483,0,532 - I'm a bit baffled about this field?
thanks for your help, Trying to get there