We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
something fishy? VCF depth and BAM depth don't match
So after performing a multisample variant calling using GATK 126.96.36.199, I separated one of the samples and wanted to visualize one heterozygous site on IGV. If you see from the attached image, the VCF shows that the Depth is 1 and the GQ is 99. But, the BAM file has lots of reads assigned to that position. I have used the original BAM file that was used during the variant calling. Is there a possibility of rearrangement at that site due to which the Depth became 1? Should have I used the rearranged BAM file instead for visualizing? If the Depth is 1 in the VCF file, how come the GQ is 99?