From a384c31925a02a7f33ddd66d7fb5a9098c5bb033 Mon Sep 17 00:00:00 2001 From: Mathias Johansson Date: Fri, 16 Feb 2024 15:37:45 +0100 Subject: [PATCH 1/2] use tumor column for filter in tumor normal --- .../variant_calling/somatic_sv_tumor_normal.rule | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule index cab852304..6e18d05fb 100644 --- a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule +++ b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule @@ -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}; """ From 330f0faf632355a954ffdd98ab312963d6c494c3 Mon Sep 17 00:00:00 2001 From: Mathias Johansson Date: Fri, 16 Feb 2024 15:56:37 +0100 Subject: [PATCH 2/2] add changelog --- CHANGELOG.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index de52f553e..465070f14 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -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]