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feat: add SVdb to TGA workflow #879

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merged 3 commits into from
Mar 9, 2022
Merged

feat: add SVdb to TGA workflow #879

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80cdf8a
svdb merge manta delly tga
khurrammaqbool Mar 8, 2022
a13deeb
update changelog
khurrammaqbool Mar 8, 2022
4a56bac
svdb merge manta delly tga
khurrammaqbool Mar 8, 2022
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2 changes: 1 addition & 1 deletion BALSAMIC/constants/workflow_params.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@
"mutation": "somatic",
"type": "SV",
"analysis_type": ["paired", "single"],
"sequencing_type": ["wgs"],
"sequencing_type": ["wgs", "targeted"],
"workflow_solution": ["BALSAMIC"],
},
}
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23 changes: 23 additions & 0 deletions BALSAMIC/snakemake_rules/annotation/varcaller_sv_filter.rule
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Expand Up @@ -73,3 +73,26 @@ rule bcftools_filter_delly:
bcftools view --threads {threads} -f .,PASS -o {output.vcf_sv_pass} -O z {input.vcf};
tabix -p vcf -f {output.vcf_sv_pass};
"""

rule bcftools_filter_svdb:
input:
vcf = vep_dir + "SV.somatic.{case_name}.svdb.all.vcf.gz",
output:
vcf_sv_pass_svdb = vep_dir + "SV.somatic.{case_name}.svdb.all.filtered.pass.vcf.gz",
benchmark:
benchmark_dir + "bcftools_filter_svdb_SV.somatic.{case_name}.svdb.vep.tsv"
singularity:
Path(singularity_image,config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
params:
case_name = "{case_name}",
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
threads:
get_threads(cluster_config, "bcftools_filter_svdb")
message:
"Filtering svdb merged Manta and Delly results for PASS variants using bcftools for sample '{params.case_name}' "
shell:
"""
bcftools view --threads {threads} -f .,PASS -o {output.vcf_sv_pass_svdb} -O z {input.vcf};

tabix -p vcf -f {output.vcf_sv_pass_svdb};
"""
6 changes: 4 additions & 2 deletions CHANGELOG.rst
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Expand Up @@ -8,9 +8,11 @@ Added:
* Call umi variants using TNscope in bed defined regions #821
* UMI duplication metrics to report in multiqc_picard_dups.json #844
* QC default validation conditions (for not defined capture kits) #855
* SVDB to the varcall_py36 container #871
* SVDB to WGS workflow #871
* SVdb to the varcall_py36 container #871
* SVdb to WGS workflow #871
* Docker container for vcf2cytosure #858
* SVdb to TGA workflow #871


Changed:
^^^^^^^^
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