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Don't put withdrawn sample data in alt_allele table [VS-369] #7762

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merged 8 commits into from
Apr 8, 2022
Merged

Don't put withdrawn sample data in alt_allele table [VS-369] #7762

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77e550f
allow for gatk to be overridden, update with known good jar
kcibul Apr 6, 2022
6c5af82
dockstore
rsasch Apr 6, 2022
cbbe7ec
added check for withdrawn samples to populate_alt_allele_table.py
rsasch Apr 6, 2022
fdd64b4
Merge branch 'ah_var_store' into rsa_alt_allele_withdrawn
rsasch Apr 6, 2022
c8b37aa
docker and dockstore
rsasch Apr 6, 2022
f530f10
Merge branch 'ah_var_store' into rsa_alt_allele_withdrawn
rsasch Apr 7, 2022
d844be7
go back to query with IN because JOIN wasn't more performant in tests
rsasch Apr 8, 2022
dd65e95
dockstore
rsasch Apr 8, 2022
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateAltAllele.wdl
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Expand Up @@ -180,7 +180,7 @@ task PopulateAltAlleleTable {
$SERVICE_ACCOUNT_STANZA
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20220211"
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_alt_allele_withdrawn_2022_04_07"
memory: "3 GB"
disks: "local-disk 10 HDD"
cpu: 1
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5 changes: 3 additions & 2 deletions scripts/variantstore/wdl/extract/populate_alt_allele_table.py
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Expand Up @@ -31,10 +31,11 @@ def populate_alt_allele_table(query_project, vet_table_name, fq_dataset, sa_key_
alt_allele_temp_function = Path('alt_allele_temp_function.sql').read_text()
alt_allele_positions = Path('alt_allele_positions.sql').read_text()
fq_vet_table = f"{fq_dataset}.{vet_table_name}"
fq_sample_info = f"{fq_dataset}.sample_info"
query_with = f"""INSERT INTO `{fq_dataset}.alt_allele`
WITH
position1 as (select * from `{fq_vet_table}` WHERE call_GT IN ('0/1', '1/0', '1/1', '0|1', '1|0', '1|1', '0/2', '0|2','2/0', '2|0')),
position2 as (select * from `{fq_vet_table}` WHERE call_GT IN ('1/2', '1|2', '2/1', '2|1'))"""
position1 as (select * from `{fq_vet_table}` WHERE call_GT IN ('0/1', '1/0', '1/1', '0|1', '1|0', '1|1', '0/2', '0|2','2/0', '2|0') AND sample_id NOT IN (SELECT sample_id from {fq_sample_info} WHERE withdrawn IS NOT NULL)),
position2 as (select * from `{fq_vet_table}` WHERE call_GT IN ('1/2', '1|2', '2/1', '2|1') AND sample_id NOT IN (SELECT sample_id from {fq_sample_info} WHERE withdrawn IS NOT NULL))"""

sql = alt_allele_temp_function + query_with + alt_allele_positions
result = utils.execute_with_retry(client, f"into alt allele from {vet_table_name}", sql)
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