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.
Picard's CollectMultipleMetrics in Queue v3.4 and v3.5
Some of the picard's collect (e.g.
CollectInsertSizeMetrics) commands load R script resources. Those resources were present in Queue <= v3.3-0 but they are absent from the subsequent versions.
$ jar tf 3.3-0/Queue.jar | grep "picard.*R$" picard/analysis/baseDistributionByCycle.R picard/analysis/gcBias.R picard/analysis/meanQualityByCycle.R picard/analysis/rnaSeqCoverage.R picard/analysis/qualityScoreDistribution.R picard/analysis/insertSizeHistogram.R $ jar tf 3.4-0/Queue.jar | grep "picard.*R$" $ jar tf 3.5-0/Queue.jar | grep "picard.*R$" $
Without those resources,
CollectMultipleMetrics throws something similar to
java.lang.IllegalArgumentException: Script [picard/analysis/qualityScoreDistribution.R] not found in classpath depending on which commands it hits first. I thought I would be able to overcome that by adding
CLASSPATH but it did not help. I had to add them to
Queue.jar in order to make it work.
It would be nice to have those resources back in the distributed