Update gatk_docker with CPX annotation changes to SVAnnotate - Githubissues

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing

BSD 3-Clause "New" or "Revised" License

170 stars 70 forks source link

Update gatk_docker with CPX annotation changes to SVAnnotate #632

Closed epiercehoffman closed 5 months ago

epiercehoffman commented 8 months ago

Updates:

SVAnnotate was recently updated to improve functional consequence annotation for complex SVs
The GATK docker for GCP and Azure is updated in this PR to a recent nightly GATK snapshot including the latest changes to SVAnnotate

Testing:

AnnotateVcf WDL & JSON validated with womtool
Tested AnnotateVcf with updated gatk_docker on GCP cromwell and verified that PREDICTED_PARTIAL_DISPERSED_DUP was present in the header and in INFO for some variants, indicating that the latest changes to SVAnnotate were applied

Update 2/23/24:

Updated again for latest changes to SVAnnotate, tested in gnomAD data