Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

vs 1372 excess alt alleles -- set limit to 3 for a test #8843

Draft
wants to merge 4 commits into
base: ah_var_store
Choose a base branch
from
Draft

vs 1372 excess alt alleles -- set limit to 3 for a test #8843

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
1509e1b
set to 3--lets see how quickstart does
RoriCremer May 22, 2024
a8b9bdb
update dockstore
RoriCremer May 22, 2024
288d0b4
use georges new gatk docker
RoriCremer May 23, 2024
8657a88
add excess alt alleles to the vcf header
RoriCremer May 23, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .dockstore.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -309,6 +309,7 @@ workflows:
branches:
- master
- ah_var_store
- rc-vs-1372-excess-alt-alleles-3-test
tags:
- /.*/
- name: GvsIngestTieout
Expand Down
2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateFilterSet.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ workflow GvsCreateFilterSet {
intervals = SplitIntervals.interval_files[i],
fq_alt_allele_table = fq_alt_allele_table,
alt_allele_table_timestamp = AltAlleleTableDatetimeCheck.last_modified_timestamp,
excess_alleles_threshold = 1000000,
excess_alleles_threshold = 3,
output_file = "${filter_set_name}_${i}.vcf.gz",
project_id = project_id,
dataset_id = dataset_name,
Expand Down
2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsUtils.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ task GetToolVersions {
String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim"
String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2024-04-22-alpine-32804b134a75"
String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024_05_10-gatkbase-9bd39afc04ae"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024_05_23-gatkbase-28d855745d35"
String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"
String gotc_imputation_docker = "us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.5-1.10.2-0.1.16-1649948623"
String plink_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/plink2:2024-04-23-slim-a0a65f52cc0e"
Expand Down
1 change: 1 addition & 0 deletions src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohort.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -237,6 +237,7 @@ private static VCFHeader generateVcfHeader(Set<String> sampleNames,

// Filter fields
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.LOW_QUAL_FILTER_NAME));
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_ALLELES));
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_HET_KEY));
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NO_HQ_GENOTYPES));

Expand Down
Loading