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Zero Depth with Genotype?

kennethhankennethhan SeoulMember
edited May 2016 in Ask the GATK team

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 .
GATK v3.5
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

GATK v3.4
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

Best Answer


  • tsanaviatsanavia Harvard Medical School, BostonMember

    Hi. I am looking at a VCF file with SNV results from Haplotype Caller, using GATK version 3.5. I've noticed one call reporting the following description 1/1:0,0:0:3:1|1:17764184_CG_C:6,3,0 (format GT:AD:DP:GQ:PGT:PID:PL). Here in attachment there is the IGV plot of both the original bam file (upper panel) and the “bamout” file re-assembled by Haplotype Caller (lower panel) at the location of that SNV.
    My guess is that the VCF reports the final genotype inferred by Haplotype Caller looking at its re-assembled bamout file, but as coverage it reports the number of reads present in the original bam file provided as input to the caller (you see one read, but its mapping quality is 6, and GATK considers only reads with mapping quality >20). Is it correct?

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    I think this issue of reporting AD/DP from the original BAM file instead of the bamout file was fixed after 3.5. If you try with the latest version, you should get the correct annotation values.


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