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fix: use correct bcftools filter column for tumor in manta tumor only #1400

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Feb 16, 2024
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fix: use correct bcftools filter column for tumor in manta tumor only #1400

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a384c31
use tumor column for filter in tumor normal
mathiasbio Feb 16, 2024
330f0fa
add changelog
mathiasbio Feb 16, 2024
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4 changes: 2 additions & 2 deletions BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule
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Expand Up @@ -49,11 +49,11 @@ python {params.tmpdir}/runWorkflow.py -m {params.runmode} -j {threads};

bgzip -l 9 {params.tmpdir}/results/variants/somaticSV_converted.vcf ;

bcftools filter --threads {threads} --exclude 'SUM(FORMAT/PR[0:1]+FORMAT/SR[0:1]) < {params.low_pr_sr_count_value}' --soft-filter '{params.low_pr_sr_count_filter_name}' --mode '+' -o {output.final} -O z {params.tmpdir}/results/variants/somaticSV_converted.vcf.gz
bcftools filter --threads {threads} --exclude 'SUM(FORMAT/PR[1:1]+FORMAT/SR[1:1]) < {params.low_pr_sr_count_value}' --soft-filter '{params.low_pr_sr_count_filter_name}' --mode '+' -o {output.final} -O z {params.tmpdir}/results/variants/somaticSV_converted.vcf.gz

tabix -p vcf -f {output.final};

echo -e \"{params.tumor}\\tTUMOR\\n{params.normal}\\tNORMAL\" > {output.namemap};
echo -e \"{params.normal}\\tNORMAL\\n{params.tumor}\\tTUMOR\" > {output.namemap};

rm -rf {params.tmpdir};
"""
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3 changes: 2 additions & 1 deletion CHANGELOG.rst
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Expand Up @@ -14,7 +14,8 @@ Removed:

Fixed:
^^^^^^
* ASCAT-Ngs container https://github.com/Clinical-Genomics/BALSAMIC/pull/1395
* ASCAT-Ngs container https://github.com/Clinical-Genomics/BALSAMIC/pull/1395
* bcftools in manta_tumor_normal uses correct column for tumor read filtering https://github.com/Clinical-Genomics/BALSAMIC/pull/1400


[13.0.1]
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