Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
GATK-HC results generate records with read depth of zero?
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?