DepthOfCoverage in GATK4.1.9.0 with -gene-list option
Hi all,
I’m trying to use the DepthOfCoverage tool with GATK 4.1.9.0. I used the "-gene-list" option but I didn't obtain the "_gene_statistics" output. However, I obtain the "_gene_summary" output correctly. I found marta r issue and thought this problem was solved after GATK 4.1.8.0.
This is the command:
gatk DepthOfCoverage \
--java-options '-Xmx28G' \
-R '/path/to/ucsc.hg19.fasta' \
-I '/path/to/file.bam' \
-L '/path/to/file.interval_list.bed' \
-gene-list '/path/to/geneTrack.refseq' \
-O '/path/to/file_DepthOfCoverage' \
--interval-padding 0
There is no error in the log output. Also, I can't use GATK 4.1.8.0 to test DepthOfCoverage in this version because I only have access to GATK 4.1.9.0.
I hope you can help me. Thanks in advance!
-
Hi David Jaspez, our team is out of office. We will look into this issue further when we return (no need to repost).
-
Hi David Jaspez,
The team looked over this issue again and it seems that we missed something and the issue has not been resolved. We will continue to post updates here and on the github issue post when we publish a fix.
Thanks for bringing it to our attention!
Genevieve
-
David Jaspez a fix will be coming out in the next GATK release: https://github.com/broadinstitute/gatk/pull/7025
-
Hi again, thank you so much! I look forward to the next release.
Please sign in to leave a comment.
4 comments