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Disable GATK filters when joint calling #1050

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Jun 1, 2023
Merged

Disable GATK filters when joint calling #1050

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f1deaf3
Disable GATK filters when joint calling
amizeranschi May 30, 2023
6b30ea8
Update CHANGELOG.md
amizeranschi May 30, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -69,6 +69,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1040](https://github.com/nf-core/sarek/pull/1040) - Fix dict channel issue due to [#1032](https://github.com/nf-core/sarek/pull/1032)
- [#1043](https://github.com/nf-core/sarek/pull/1043) - Fix typo in the tags.yml files from [#978](https://github.com/nf-core/sarek/pull/978)
- [#1048](https://github.com/nf-core/sarek/pull/1048) - Skip tool validation on annotation to fix [#949](https://github.com/nf-core/sarek/issues/949), check that bam is bam and cram is cram [#895](https://github.com/nf-core/sarek/issues/895)
- [#1050](https://github.com/nf-core/sarek/pull/1050) - Disable GATK VCF filters when joint calling to fix [#1025](https://github.com/nf-core/sarek/issues/1025)

### Removed

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2 changes: 1 addition & 1 deletion subworkflows/local/bam_variant_calling_germline_all/main.nf
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Expand Up @@ -122,7 +122,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
known_snps_vqsr,
intervals,
intervals_bed_combined_haplotypec,
(skip_tools && skip_tools.split(',').contains('haplotypecaller_filter')))
((skip_tools && skip_tools.split(',').contains('haplotypecaller_filter') || joint_germline)))

vcf_haplotypecaller = BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.vcf
versions = versions.mix(BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.versions)
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