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Fix varscan #84

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merged 3 commits into from
Apr 1, 2024
Merged

Fix varscan #84

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e2ad505
fix: varscan issue
dnousome Mar 28, 2024
197b148
fix: correct mutect ordering
dnousome Mar 29, 2024
d99e7d2
fix: mutect paired ordering
dnousome Apr 1, 2024
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3 changes: 2 additions & 1 deletion workflow/rules/somatic_snps.paired.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -294,7 +294,8 @@ rule mutect_filter:
# VarScan can output ambiguous IUPAC bases/codes
# the awk one-liner resets them to N, from:
# https://github.com/fpbarthel/GLASS/issues/23
bcftools sort -T ${{tmp}} "{output.final}" \\
bcftools view -s "{params.tumorsample}","{params.normalsample}" {output.final} \\
| bcftools sort -T ${{tmp}} - \\
| bcftools norm --threads {threads} --check-ref s -f {params.genome} -O v \\
| awk '{{gsub(/\y[W|K|Y|R|S|M|B|D|H|V]\y/,"N",$4); OFS = "\t"; print}}' \\
| sed '/^$/d' > {output.norm}
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5 changes: 3 additions & 2 deletions workflow/rules/somatic_snps.tumor_only.smk
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Expand Up @@ -165,7 +165,8 @@ rule mutect_filter_single:
# VarScan can output ambiguous IUPAC bases/codes
# the awk one-liner resets them to N, from:
# https://github.com/fpbarthel/GLASS/issues/23
bcftools sort -T ${{tmp}} "{output.final}" \\
bcftools view -s "{params.tumorsample}" {output.final} \\
| bcftools sort -T ${{tmp}} - \\
| bcftools norm --threads {threads} --check-ref s -f {params.genome} -O v \\
| awk '{{gsub(/\y[W|K|Y|R|S|M|B|D|H|V]\y/,"N",$4); OFS = "\t"; print}}' \\
| sed '/^$/d' > {output.norm}
Expand Down Expand Up @@ -342,7 +343,7 @@ rule varscan_filter_single:
--output {output.filtered}

samplesFile="{output.samplesfile}"
echo -e "TUMOR\t{params.tumorsample}\n" > "{output.samplesfile}"
echo -e "Sample1\t{params.tumorsample}\n" > "{output.samplesfile}"

bcftools reheader \\
-o "{output.final}" \\
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