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.
Hi I'm using the Haplotypecaller 3.4 in my pipeline, and I've detected this Issue. Depth is 37, with such a huge quality and when looking at the last column I see a GT 1/1 suported by an AD of 0,0 and a DO o 0.
Have you noticed this? If so, has this been corrected in 3.5?
It is giving me problems with other steps as depth is 0.
chr11 10823576 . C CACACTCCTAAAATAGTTTCATGTTTTAATAGCAAATGAAATCACATATATTGCAGAATTTAACATTTGTTGCCTAA 5199.77 PASS DP=37;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,0:0:99:5180,332,0