Hello Members,
I am trying to understand the calculations that goes into QD in GATK. NOTE: I already searched around and did not find answer:
Here its explained but that is no longer valid with recent versions of GATK: http://gatkforums.broadinstitute.org/discussion/2062/how-do-you-calculate-qd
In the following its mentioned that the new versions calculate QD using AD: https://www.broadinstitute.org/gatk/blog?id=3862
None of the above is helping. In joint VCF file I have following entry:
1 5474238 . C A 163.45 PASS AC=2;AF=0.071;AN=28;DP=609;FS=0.000;MQ=60.00;MQ0=0;QD=27.05;Samples=2500NA12878v1PCRfree1;VQSLOD=18.21;VariantType=SNP;culprit=MQ GT:AD:GQ:PL 1/1:0,3:12:175,12,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,0 0/0:0,0:0:0,0,00/0:0,0:0:0,0,0
The QD is 27.05, QUAL: 163.45 and AD is 3
In the individual GVCF files (all 14) I search for Chromosome 1 and Position 5474238, and there only one entry:
1 5474238 . C A,<NON_REF> 142.28 . DP=3;MLEAC=2,0;MLEAF=1.00,0.00;MQ=60.00;MQ0=0 GT:AD:GQ:PL:SB 1/1:0,3,0:12:175,12,0,175,12,175:0,0,2,1
Here the QUAL is 142.28 and AD is 3. How come in the joint VCF file, the QUAL becomes 163.45 and QD=27.05 with DP=609?
GATK Version=3.2-2-gec30cee
Thanks in Advance
Deep
