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**GATK4-BETA.2** is here. That's TWO, as in the second beta release. Be sure to read about the known issues before test driving. See Article#9881 to start and https://github.com/broadinstitute/gatk/blob/master/README.md for details.

# Picard CollectOxoGMetrics

Salt Lake City, UTMember

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?
Thanks!

Tagged:

Issue Number
274
State
closed
Last Updated
Assignee
Array
Milestone
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Closed By
dekling