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Zero Depth with Genotype?
I'm using GATK and I found this - "zero depth with genotype"
As INFO column said, DP=54, however, in sample column DP:0 with GT:1/1.
And reads are found by looking bam file with samtools tview.
Could you help me how to interpret this?
Kenneth Joohyun Han
ps. this is found both GATK v3.5 and v3.4 .
chr3 150421527 . C CTCCTCCTCCTCCTCCACCTCT 408.76 PASS AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;SOR=0.693;set=variant2 GT:AD:DP:GQ:PL 1/1:0,0:0:22:446,22,0
chr3 150421527 . C CTCCTCCTCCTCCTCCACCTCT 417.79 PASS AC=2;AF=1.00;AN=2;DP=54;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;SOR=0.693;set=variant2 GT:AD:DP:GQ:PL 1/1:0,0:0:22:446,22,0