Notice:
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.

GATK didn't Output the InDel I expected

Hi! I used GATK to call InDel and SNP with my sequence data. But GATK didn't give any output variations(InDel and SNP).
So, I use GATK to generate a "bamout file" showing how HaplotypeCaller has remapped sequence reads(-disableOptimizations -forceActive -dt NONE).
The bottom bam file is the Input bam file and the top bam file is the HaplotypeCaller has remapped bam. I've checkd the base quality and mapping quality and there was no problem.

Why did GATK this remaping ? And Is this a bug?

Answers

Sign In or Register to comment.