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Reimplement ParseGenotypes in GenotypeComplexVariants
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Update docker

Fix errors

Update dockers

Fix sort in wdl

Fix alt alleles

Perfect parity

Update dockers

Remove UNRESOLVED filter status

Delete unused scripts
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@mwalker174
mwalker174 committed Oct 23, 2023
1 parent 8bcdb15 commit d25f104
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Showing 5 changed files with 1,188 additions and 1,157 deletions.
12 changes: 6 additions & 6 deletions inputs/values/dockers.json
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"samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2023-07-28-v0.28.1-beta-e70dfbd7",
"sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2023-07-28-v0.28.1-beta-e70dfbd7",
"sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/vjalili/sv-base-mini:5994670",
"sv_pipeline_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
"sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
"sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
"sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
"sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
"sv_pipeline_rdtest_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
"sv_pipeline_base_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-posthoc-cpx-8a3d8047",
"sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-posthoc-cpx-8a3d8047",
"sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-posthoc-cpx-8a3d8047",
"sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-posthoc-cpx-8a3d8047",
"sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-posthoc-cpx-8a3d8047",
"sv_pipeline_rdtest_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-posthoc-cpx-8a3d8047",
"wham_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/wham:2023-07-28-v0.28.1-beta-e70dfbd7",
"igv_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
"duphold_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",
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