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GATK-HC results generate records with read depth of zero?

vanvan CalifroniaMember

Dear all,

I ran GATK3.6 and noticed that few records from the Haplotype Caller happen to contain read depth as zero in the FORMAT field. Below is one instance:
chr2 208630795 . T TA,TAA 0.39 . DP=16;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=46240.00;INS GT:AD:DP:GQ:PL:SB 1/1:0,0,0:0:0:18,3,0,3,0,0:0,0,0,0

The genotype called is 1/1 and the INFO field has DP=16, so not sure how to interpret this line in the vcf if you needed to look into Allele depth as well. Could some one help me with this issue?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I think this has to do with phased variants. Can you please post IGV screenshots of the original BAM file and bamout file here? Please include ~300 bases before and after the site of interest.


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