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feat: add triallelic_sites and variants with MaxDepth #1021

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merged 5 commits into from
Nov 16, 2022
Merged

feat: add triallelic_sites and variants with MaxDepth #1021

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dfc494a
refactor toml and add samtools index
khurrammaqbool Nov 16, 2022
e62aab4
changelog
khurrammaqbool Nov 16, 2022
80c30aa
add variants
khurrammaqbool Nov 16, 2022
59f32ea
changelog
khurrammaqbool Nov 16, 2022
51a4720
add triallelic_sites to umi
khurrammaqbool Nov 16, 2022
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2 changes: 1 addition & 1 deletion BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_normal.rule
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ bcftools view {input.vcf} \

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

bcftools view -f PASS -o {output.vcf_pass_TNscope_umi}.temp -O z {output.vcf_filtered};
bcftools view -f PASS,triallelic_site -o {output.vcf_pass_TNscope_umi}.temp -O z {output.vcf_filtered};

python {params.edit_vcf_script} \
--input_vcf {output.vcf_pass_TNscope_umi}.temp \
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2 changes: 1 addition & 1 deletion BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ bcftools view {input.vcf} \

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

bcftools view -f PASS -o {output.vcf_pass_TNscope_umi}.temp -O z {output.vcf_filtered};
bcftools view -f PASS,triallelic_site -o {output.vcf_pass_TNscope_umi}.temp -O z {output.vcf_filtered};

python {params.edit_vcf_script} \
--input_vcf {output.vcf_pass_TNscope_umi}.temp \
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4 changes: 2 additions & 2 deletions BALSAMIC/snakemake_rules/annotation/varcaller_sv_filter.rule
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Expand Up @@ -21,7 +21,7 @@ rule bcftools_filter_sv_research:
"Filtering merged research structural and copy number variants using bcftools for {params.case_name}"
shell:
"""
bcftools view --threads {threads} -f .,PASS -o {output.vcf_pass_svdb_research} -O z {input.vcf_sv_research};
bcftools view --threads {threads} -f .,PASS,MaxDepth -o {output.vcf_pass_svdb_research} -O z {input.vcf_sv_research};

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

Expand All @@ -48,7 +48,7 @@ rule bcftools_filter_sv_clinical:
"Filtering merged clinical structural and copy number variants using bcftools for {params.case_name}"
shell:
"""
bcftools view --threads {threads} -f .,PASS -o {output.vcf_pass_svdb_clinical} -O z {input.vcf_sv_clinical};
bcftools view --threads {threads} -f .,PASS,MaxDepth -o {output.vcf_pass_svdb_clinical} -O z {input.vcf_sv_clinical};

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

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4 changes: 2 additions & 2 deletions BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_normal.rule
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Expand Up @@ -26,7 +26,7 @@ rule bcftools_filter_tnscope_research_tumor_normal:
"""
bcftools view {input.vcf_snv_research} \
| bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' \
| bcftools view -f PASS -o {output.vcf_pass_tnscope_research} -O z;
| bcftools view -f PASS,triallelic_site -o {output.vcf_pass_tnscope_research} -O z;

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

Expand Down Expand Up @@ -54,7 +54,7 @@ rule bcftools_filter_tnscope_clinical_tumor_normal:
shell:
"""
bcftools view {input.vcf_snv_clinical} \
| bcftools view -f PASS -o {output.vcf_pass_tnscope_clinical} -O z;
| bcftools view -f PASS,triallelic_site -o {output.vcf_pass_tnscope_clinical} -O z;

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

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4 changes: 2 additions & 2 deletions BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_only.rule
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ bcftools view -f PASS --threads {threads} --regions-file {input.wgs_calling_file
| bcftools filter --threads {threads} --include 'SUM(FORMAT/QSS)/SUM(FORMAT/AD) >= {params.qss[0]}' --soft-filter '{params.qss[1]}' --mode '+' \
| bcftools filter --threads {threads} --include 'FORMAT/ALT_F1R2 > {params.strand_reads[0]} && (FORMAT/ALT_F1R2 > 0 && FORMAT/ALT_F2R1 > {params.strand_reads[0]} && FORMAT/REF_F1R2 > {params.strand_reads[0]} && FORMAT/REF_F2R1 > {params.strand_reads[0]})' --soft-filter '{params.strand_reads[1]}' --mode '+' \
| bcftools filter --threads {threads} --include "INFO/SOR < {params.sor[0]}" --soft-filter '{params.sor[1]}' --mode '+' \
| bcftools view -f PASS -o {output.vcf_pass_tnscope_research} -O z;
| bcftools view -f PASS,triallelic_site -o {output.vcf_pass_tnscope_research} -O z;

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

Expand Down Expand Up @@ -73,7 +73,7 @@ rule bcftools_filter_tnscope_clinical_tumor_only:
grep -v '^@' {input.wgs_calling_file} > {input.wgs_calling_file}.bed

bcftools view -f PASS --threads {threads} --regions-file {input.wgs_calling_file}.bed {input.vcf_snv_clinical} \
| bcftools view -f PASS -o {output.vcf_pass_tnscope_clinical} -O z;
| bcftools view -f PASS,triallelic_site -o {output.vcf_pass_tnscope_clinical} -O z;

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

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3 changes: 2 additions & 1 deletion CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ Added:
* Annotation of snv_clinical_observations for somatic snv https://github.com/Clinical-Genomics/BALSAMIC/pull/1012
* Annotation of sv_clinical_observations for somatic sv and SV CNV filter rules https://github.com/Clinical-Genomics/BALSAMIC/pull/1013
* Swegen SNV and SV frequency database for WGS https://github.com/Clinical-Genomics/BALSAMIC/pull/1014
* triallelic_sites and variants with MaxDepth to the VCFs https://github.com/Clinical-Genomics/BALSAMIC/pull/1021

Changed:
^^^^^^^^
Expand All @@ -29,7 +30,7 @@ Changed:
Fixed:
^^^^^^
* Reverted `pandas` version (from `1.3.5` to `1.1.0`) https://github.com/Clinical-Genomics/BALSAMIC/pull/1018
* samtools command in merge bam and names in toml for vcfanno https://github.com/Clinical-Genomics/BALSAMIC/pull/10
* samtools command in merge bam and names in toml for vcfanno https://github.com/Clinical-Genomics/BALSAMIC/pull/1020

Removed:
^^^^^^^
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