Update GVS sample QC to support multiple callsets per datasset [VS-177] #7451
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rsasch
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ahaessly
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Sep 8, 2021
| @@ -66,7 +66,7 @@ SELECT "$NAME_OF_FILTER_SET" filter_set_name, | |||
| CASE WHEN INSTR(call_GT, "0") > 0 THEN "het" ELSE "homvar" END as gt_type, -- if GT contains a zero, its a het | |||
| titv(ref, alt) as titv, | |||
| CASE WHEN gnomad.location IS NULL THEN false ELSE true END in_gnomad | |||
| FROM `$FQ_DATASET.vet_all` v | |||
| FROM `$FQ_VET_ALL` v | |||
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I think you either need to add FQ_VET_ALL to the README instructions or use a variable like: $FQ_PREFIX_vet_all
scripts/variantstore/callset_QC/filter_set_samples_create_metrics.example.sql
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Thanks for catching those! Changed so that only $FQ_PREFIX and $NAME_OF_FILTER_SET are used in the SQL and README. |
RoriCremer
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Sep 20, 2021
This was referenced Mar 17, 2023
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Closes https://broadworkbench.atlassian.net/browse/VS-177