Update RegenotypeCNVs.wdl GetRegenotype task#839
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knathamuni wants to merge 1 commit intobroadinstitute:mainfrom
Open
Update RegenotypeCNVs.wdl GetRegenotype task#839knathamuni wants to merge 1 commit intobroadinstitute:mainfrom
knathamuni wants to merge 1 commit intobroadinstitute:mainfrom
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I updated the GetRegenotype task by taking the bash script in the code block and converting it to python to improve runtime efficiency. This fix will be especially helpful for poorer quality samples running through GATK-SV.
This is a successful run from my cohort:(https://app.terra.bio/#workspaces/pregnancy-loss/FGC_Talkowski_Barnett_Scott_WGS_KN/submission_history/84d48ece-8797-4ea0-a006-2d418eec2085)
This is a successful run of 1KGP using my new workflow: (https://app.terra.bio/#workspaces/prenatal-wgs/gatk-sv-pipeline-1kgp-KN-testing/submission_history/fc508772-a308-4154-9e74-88d032a84637)
The outputs looks identical