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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Parallelize processing individual samples for Variant calling
I have 190 samples that I am running through the GATK DNAseq pipeline following the Best Practices. Since only a few genes have been sequenced for each sample, the alignment files are very small (0.5 GB BAM files), but even then processing each samples takes about 3 hours. Is there a way to parallelize the processing of the individual samples on a mutli-core machine (since processing each sample is independent of each other it should not make a difference). There is a feature in Python using Pool in the multiprocessing module that could be used. I tried it but it does not seem to work for me. Does the GATK team have any guidance or information on this issue.