Dear Developers,
I called the variants with Mutect2, GATK4 (beta). Reading the file header, I see that it suppese to have AD and DP
FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
However, after examining the content of FORMAT field (highlighted), I see DP nowhere.
Example is given below. Am I missing something?
Thank you
Vlad
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample-N sample-T
1 172415451 rs2269615 C T . PASS DB;DP=592;ECNT=2;NLOD=41.53;N_ART_LOD=-2.159e+00;POP_AF=1.000e-03;P_GERMLINE=-3.822e+01;TLOD=9.50 _GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:MBQ:MCL:MFRL:MMQ:MPOS:REF_F1R2:REF_F2R1:SA_MAP_AF:SA_POST_PROB _0/0:138,0:0.960,0.040:0:0:NaN:32,0:0,0:158,0:60,0:26,0:74:64 0/1:445,8:0.963,0.037:2:6:0.750:32,33:0,0:157,162:60,60:25,22:224:221:0.020,0.010,0.018:1.504e-03,5.110e-03,0.993