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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.
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?