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VS-1754. Remove a (now non-existent) clinvar significance from expected. #9284

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Merged
merged 1 commit into from
Oct 16, 2025
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VS-1754. Remove a (now non-existent) clinvar significance from expected. #9284

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1 change: 1 addition & 0 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -344,6 +344,7 @@ workflows:
- master
- ah_var_store
- vs_1634_pgen_exome
- gg_VS-1754_RemoveOneClinvarSignificanceFromTest
tags:
- /.*/
- name: GvsIngestTieout
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4 changes: 1 addition & 3 deletions scripts/variantstore/variant-annotations-table/GvsValidateVAT.wdl
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Expand Up @@ -1101,7 +1101,6 @@ task ClinvarSignificance {
# "risk factor",
# "protective",
# "affects",
# "conflicting data from submitters",
# "other",
# "not provided"]
Expand All @@ -1114,7 +1113,6 @@ task ClinvarSignificance {
echo 'affects
association
benign
conflicting data from submitters
drug response
likely benign
likely pathogenic
Expand All @@ -1125,7 +1123,7 @@ task ClinvarSignificance {
risk factor
uncertain significance' > expected_clinvar_classes.txt
comm -23 <(sort bq_clinvar_classes.txt) expected_clinvar_classes.txt > missing_clinvar_classes.txt
comm -13 <(sort bq_clinvar_classes.txt) expected_clinvar_classes.txt > missing_clinvar_classes.txt
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This looks to have been wrong in the original implementation.

NUMRESULTS=$( wc -l bq_clinvar_classes.txt | awk '{print $1;}' ) # we expect this to be 13+
NUMMISS=$( wc -l missing_clinvar_classes.txt | awk '{print $1;}' ) # we expect this to be 0
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