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:AD:DP:GQ:PL 0/1:19,17:36:87.16:483,0,532
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
Thanks for the link but I have been there also. That for the AD definition. I understand that PL is phred-scaled genotype likelihood but why are there three values? Thanks
Also why are the two genotype quality values thanks
There is only one GQ value. It is 87.16 (87 and 16/100)