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.
Hi there, I'm having trouble getting picard's CollectOxoGMetrics to produce output. Specifically, commands like:
java -Xmx2g -jar ~/tools/picard-tools-1.140/picard.jar CollectOxoGMetrics I=test.bam O=test.oxog.csv R=~/resources/GRCh38.p2.fa
produces a "test.oxog.csv" file with some header information including the command line arguments, etc., but no other content besides a few blank lines. No warning or error information is emitted, and other metrics commands seem to work just fine. I've tried a couple of different bams now (one in-house generated, one from Illumina) and got the same results for each one.
Am I missing something obvious?