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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
https://broadinstitute.github.io/gatk-sv/
BSD 3-Clause "New" or "Revised" License
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GWAS-SVs pipeline Module 7 #521

Open tanxiangyu opened 1 year ago

tanxiangyu commented 1 year ago

We encountered some troubles in the process of testing the GWAS-SVs pipeline with the GATK due to the lack of JSON files for module7. I wonder if you can share the JSON file in Module 7 (in development) of the SVs analysis (https://github.com/broadinstitute/gatk-sv#merge-batch-sites). Thank you very much for your attention and consideration. Looking forward to your reply.

epiercehoffman commented 1 year ago

I assume you mean the downstream filtering workflows rather than the MergeBatchSites workflow you linked (just in case, the MergeBatchSites JSON is here: https://github.com/broadinstitute/gatk-sv/blob/main/inputs/templates/test/MergeBatchSites/MergeBatchSites.json.tmpl). As noted in #460, we are currently working on the downstream filtering workflows. This is a priority for us and we hope to be able to share best practices for those very soon.