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Update gatk_docker with CPX annotation changes to SVAnnotate #632

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merged 3 commits into from
Apr 29, 2024

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epiercehoffman
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@epiercehoffman epiercehoffman commented Jan 30, 2024

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

@@ -2,7 +2,7 @@
"name": "dockers",
"cnmops_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/cnmops:2024-01-24-v0.28.4-beta-9debd6d7",
"condense_counts_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
"gatk_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/gatk:2024-01-15-4.5.0.0-3-gb68fadc5f-NIGHTLY-SNAPSHOT",
"gatk_docker": "uus.gcr.io/broad-dsde-methods/eph/gatk:2024-02-16-4.5.0.0-8-gcfd4d87ec-NIGHTLY-SNAPSHOT",
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Suggested change
"gatk_docker": "uus.gcr.io/broad-dsde-methods/eph/gatk:2024-02-16-4.5.0.0-8-gcfd4d87ec-NIGHTLY-SNAPSHOT",
"gatk_docker": "us.gcr.io/broad-dsde-methods/eph/gatk:2024-02-16-4.5.0.0-8-gcfd4d87ec-NIGHTLY-SNAPSHOT",

Is that a typo?

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Yes - fixed like 3 minutes ago

@mwalker174 mwalker174 merged commit d9b5243 into main Apr 29, 2024
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@mwalker174 mwalker174 deleted the eph_svannotate_cpx_gatk_docker branch April 29, 2024 17:30
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2 participants