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 October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
MarkDuplicateSpark is slower than normal MarkDuplicates
I was happy to hear that MarkDuplicatesSpark is out of Beta now in Version 4.1. So I tested it on one of our WES samples. Unfortunatelly it took 2 times as long as the normal MarkDuplicate. Here are the two comands I used:
gatk MarkDuplicatesSpark -I '/media/Berechnungen/0028-19.recal.bam' -O '/media/Berechnungen/0028-19.dedup.bam' --metrics-file '/media/Berechnungen/0028-19.metrics' --spark-master local --verbosity ERROR --tmp-dir /media/Ergebnisse/picardtmp/
gatk MarkDuplicates -I '/media/Berechnungen/0028-19.recal.bam' -O '/media/Berechnungen/0028-19.dedup.bam' -M '/media/Berechnungen/0028-19.metrics' --TMP_DIR /media/Ergebnisse/picardtmp/
Did I do something wrong in parallelization?