We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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 for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
"Could not open array genomicsdb_array at workspace" from GenotypeGVCFs in GATK 188.8.131.52
I experience Issues with GenotypeGVCFs and GenomicsDB input in the final GATK4 release using the official Docker image. This does not occur using the 4.beta.6 release. It looks like there has been a bug in an earlier beta release with the same error message which got fixed. Is my issue related to that old bug or just results in the same error message? What can I do to debug the issue?
2018-01-10T12:15:04.154516155Z terminate called after throwing an instance of 'VariantQueryProcessorException' 2018-01-10T12:15:04.154547266Z what(): VariantQueryProcessorException : Could not open array genomicsdb_array at workspace: /keep/d22f668d4f44631d98bc650d582975ca+1399/chr22_db 2018-01-10T12:15:04.154561314Z 2018-01-10T12:15:04.620517615Z Using GATK wrapper script /gatk/build/install/gatk/bin/gatk 2018-01-10T12:15:04.620517615Z Running: 2018-01-10T12:15:04.620517615Z /gatk/build/install/gatk/bin/gatk GenotypeGVCFs -V gendb:///keep/d22f668d4f44631d98bc650d582975ca+1399/chr22_db --output chr22_db.vcf --reference /keep/db91e5f04cbd9018e42708316c28e82d+2160/hg19.fa