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.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

How to merge interval files generated from RealignerTargetCreator

golharamgolharam ✭✭✭Member ✭✭✭
edited August 2012 in Ask the GATK team

Hi all - I'm using GATK realigner which can take several hours on my samples. I'm trying to optimize my pipeline by dividing this up by chromosome for each node in my cluster. I can call RealignerTargetCreator using the -L parameter for each chromosome which results in a bunch of interval files. Now, I either want to call IndelRealigner using the -L parameter for each chromsome then merge the resulting BAM files, or merge the interval files into one then call IndelRealigner.

1) I don't see a way to merge interval files using GATK. Is this possible?

or

2) Can I call IndelRealigner and process each chromosome separately then merge the resulting BAM files together?

Best Answer

Answers

Sign In or Register to comment.