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Picard CollectOxoGMetrics

brofallonbrofallon Salt Lake City, UTMember Posts: 3

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?

Issue · Github
by Geraldine_VdAuwera

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Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,414 admin

    Hi there, sorry for the delay -- your question slipped through our net. We'll get an answer to you tomorrow.

    Geraldine Van der Auwera, PhD

  • brofallonbrofallon Salt Lake City, UTMember Posts: 3

    Thanks - indeed it was the read group issue. Looks like CollectOxoGMetrics doesn't warn about this if no read group is specified. Thanks for the assistance!

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