From 98143c5bc91d9d0ca27f9bbcbeac670cf26f0dc0 Mon Sep 17 00:00:00 2001 From: RoriCremer <6863459+RoriCremer@users.noreply.github.com> Date: Mon, 2 Aug 2021 14:52:30 -0400 Subject: [PATCH] Create VAT scripts directory (#7386) * just an initial note on the VAT---more documentation needed * create vat scripts dir and move in template --- scripts/variantstore/README.md | 8 ++++++++ .../custom_annotations_template.tsv | 0 2 files changed, 8 insertions(+) rename custom_annotations_template.tsv => scripts/variantstore/variant_annotations_table/custom_annotations_template.tsv (100%) diff --git a/scripts/variantstore/README.md b/scripts/variantstore/README.md index a82a2818bad..a513f7a230d 100644 --- a/scripts/variantstore/README.md +++ b/scripts/variantstore/README.md @@ -14,3 +14,11 @@ After using the json file to auth as that service account, you can query the # use a query like this to get the total number of bytes billed bq --project_id query --use_legacy_sql=false 'select sum(total_bytes_billed) as total from `region-us`.INFORMATION_SCHEMA.JOBS_BY_USER where creation_time > "2021-04-16 00:00:00" and creation_time < "2021-04-18 00:00:00" and total_bytes_billed > 1 limit 100' + + +### Running the VAT pipeline +The VAT pipeline is a set of WDLs +GvsSitesOnlyVCF.wdl +GvsValidateVAT.wdl + +The pipeline takes in a jointVCF and outputs a table in BigQuery diff --git a/custom_annotations_template.tsv b/scripts/variantstore/variant_annotations_table/custom_annotations_template.tsv similarity index 100% rename from custom_annotations_template.tsv rename to scripts/variantstore/variant_annotations_table/custom_annotations_template.tsv