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a strange varinat from HC
Hello GATK team,
- I've noticed a strange variant in the gvcf output of HC:
6 32552140 rs17882663 T A, 108.18 . DB;DP=0;MLEAC=2,0;MLEAF=1.00,0.00;MQ=0.00;MQ0=0 GT:GQ:PGT:PID:PL:SB 1/1:9:0|1:32552059_G_T:135,9,0,135,9,135:0,0,0,0
6 32552140 rs17882663 T A 107.28 . AC=2;AF=1.00;AN=2;DB;DP=0;FS=0.000;GQ_MEAN=9.00;MLEAC=2;MLEAF=1.00;MQ=0.00;MQ0=0;NCC=0;SOR=0.693 GT:AD:GQ:PGT:PID:PL 1/1:0,0:9:1|1:32552059_G_T:135,9,0
The DP and AD are 0, but there is a variant - A.
What do you think? Why does it happened?
- What is the difference between the DP in the format part and in the info part? I looked for an answer in the documentation, but couldn't find one. Bellow is an example of a big difference between the values of this two.
3 195511214 . G GACCTGTGGATGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTC 673.77 . AC=1;AF=0.500;AN=2;DP=169;FS=0.000;GQ_MEAN=38.00;MLEAC=1;MLEAF=0.500;MQ=56.57;MQ0=0;NCC=0;SOR=0.693 GT:AD:DP:GQ:PL 0/1:0,0:0:38:702,0,38