The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Variants with AD 0,0 and DP 0
I was investigating why some of the variants in my vcf produced with HaplotypeCaller miss some fields such as QD, DP, MQ, MQRankSum, BaseQRankSum.
I understood why by searching this forum, some of these values need other parameter to be present to be calculated, such as AD which is needed to calculate QD and so on.
So I realized that for all the variants that miss these fields I have the same GT:AD:DP values of 1/1:0,0:0, therefore AD is always 0,0 and DP 0
I read about informative and uninformative reads; some posts suggest that AD do not include uninformative reads, but DP does. By reading the documentation of DepthPerSampleHC seems like that DP in the FORMAT only includes informative reads like AD, but in the INFO has all unfiltered reads supporting that call.
why there is not the DP tag in the INFO column but only in the FORMAT for some calls?
why are these variants called if AD:DP 0,0:0 and DP in the INFO is missing?
I report an example:
Qrob_H2.3_Sc0001210 5578 . G T 18.59 . AC=2;AF=1.00;AN=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,0:0:3:45,3,0
A call with complete info is:
Qrob_H2.3_Sc0001407 1861 . A G 739.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.371;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.87;MQRankSum=-1.787;QD=30.87;ReadPosRankSum=0.240;SOR=1.609 GT:AD:DP:GQ:PL 0/1:2,19:21:27:768,0,27
It is only one sample, I know it is not enough; I am actually trying and learning how to use the variant calling pipeline for the first time before I run it on all my data; it just a test but I would like to understand this.
I apologize if this is a repetitive question; I have searched the forums and got a few hints but did not obtain a satisfactory answer.