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Update to latest version of ah_var_store gatk override jar #7793

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Apr 20, 2022
Merged

Update to latest version of ah_var_store gatk override jar #7793

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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateFilterSet.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ workflow GvsCreateFilterSet {
Array[String] snp_recalibration_annotation_values = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"]

File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220406/gatk-package-4.2.0.0-480-gb62026a-SNAPSHOT-local.jar"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220415/gatk-package-4.2.0.0-492-g1387d47-SNAPSHOT-local.jar"
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this is at least a couple of revisions back now so it wouldn't be picking up the zero-padding improvements from #7783

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True - I'll rebuild it - but the only gatk jar improvements in 7783 were really just cleaning up some logging.

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oh yeah you're right... wow did I misremember that code 😅

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in an ideal world, I think we would also create these ahead of our releases and have one named for the release---so we'd have a Charlie jar (though we've re-made it a few times over the last few weeks....)


Int? INDEL_VQSR_max_gaussians_override = 4
Int? INDEL_VQSR_mem_gb_override
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsImportGenomes.wdl
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Expand Up @@ -13,7 +13,7 @@ workflow GvsImportGenomes {
File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
Int? load_data_preemptible_override
Int? load_data_maxretries_override
File? load_data_gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220406/gatk-package-4.2.0.0-480-gb62026a-SNAPSHOT-local.jar"
File? load_data_gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220415/gatk-package-4.2.0.0-492-g1387d47-SNAPSHOT-local.jar"
String? service_account_json_path
}

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