fix: Incorrect raw TNscope delivered VCF (#1042)

Clinical-Genomics · Dec 5, 2022 · bf84c9c · bf84c9c
1 parent dc4cc9e
commit bf84c9c
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Showing 5 changed files with 19 additions and 14 deletions.
diff --git a/BALSAMIC/constants/workflow_rules.py b/BALSAMIC/constants/workflow_rules.py
@@ -135,8 +135,7 @@
     "vep_germline_normal",
     "vcfheader_rename_germline",
     # SNVs
-    "sentieon_TNscope_tumor_only",
-    "sentieon_TNscope",
+    "bcftools_view_split_variant",
     "bcftools_filter_tnscope_research_tumor_only",
     "bcftools_filter_tnscope_research_tumor_normal",
     "bcftools_filter_tnscope_clinical_tumor_only",

diff --git a/BALSAMIC/snakemake_rules/variant_calling/sentieon_split_snv_sv.rule b/BALSAMIC/snakemake_rules/variant_calling/sentieon_split_snv_sv.rule
@@ -8,13 +8,14 @@ rule bcftools_view_split_variant:
         ref = config["reference"]["reference_genome"],
         vcf = vcf_dir + "sentieon_tnscope/ALL.somatic." + config["analysis"]["case_id"] + ".tnscope.vcf.gz",
     output:
-        vcf_snv = vcf_dir + "SNV.somatic." + config["analysis"]["case_id"] + ".tnscope.vcf.gz",
-        vcf_sv = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".tnscope.research.vcf.gz",
+        vcf_tnscope = vcf_dir + "SNV.somatic." + config["analysis"]["case_id"] + ".tnscope.vcf.gz",
+        vcf_tnscope_sv = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".tnscope.research.vcf.gz",
     benchmark:
         Path(benchmark_dir,'bcftools_view_split_variant_' + config[ "analysis" ][ "case_id" ] + ".tsv").as_posix()
     singularity:
         Path(singularity_image, config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
     params:
+        housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
         tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
         case_name = config["analysis"]["case_id"]
     threads:
@@ -26,9 +27,9 @@ rule bcftools_view_split_variant:
 export TMPDIR={params.tmpdir};
 mkdir -p {params.tmpdir};
 
-bcftools view --include 'INFO/SVTYPE=="."' -O z -o {output.vcf_snv} {input.vcf}; 
-tabix -p vcf -f {output.vcf_snv};
+bcftools view --include 'INFO/SVTYPE=="."' -O z -o {output.vcf_tnscope} {input.vcf}; 
+tabix -p vcf -f {output.vcf_tnscope};
 
-bcftools view --include 'INFO/SVTYPE!="."' -O z -o {output.vcf_sv} {input.vcf}; 
-tabix -p vcf -f {output.vcf_sv};
+bcftools view --include 'INFO/SVTYPE!="."' -O z -o {output.vcf_tnscope_sv} {input.vcf}; 
+tabix -p vcf -f {output.vcf_tnscope_sv};
         """
diff --git a/BALSAMIC/snakemake_rules/variant_calling/sentieon_t_varcall.rule b/BALSAMIC/snakemake_rules/variant_calling/sentieon_t_varcall.rule
@@ -87,7 +87,7 @@ rule sentieon_TNhaplotyper_tumor_only:
         Path(benchmark_dir, "sentieon_TNhaplotyper_tumor_only_" + config["analysis"]["case_id"] + ".tsv").as_posix()
     params:
         tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
-        tumor = "TUMOR", 
+        tumor = "TUMOR",
         pon = " " if get_pon(config) is None else " ".join(["--pon", get_pon(config)]),
         pcr_model = params.common.pcr_model,
         sentieon_exec = config["SENTIEON_EXEC"],
@@ -134,10 +134,9 @@ rule sentieon_TNscope_tumor_only:
     benchmark:
         Path(benchmark_dir, "sentieon_TNscope_tumor_only_" + config["analysis"]["case_id"] + ".tsv").as_posix()
     params:
-        housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
         tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
-        tumor = "TUMOR", 
-        tumor_options = VARCALL_PARAMS["tnscope"]["tumor"], 
+        tumor = "TUMOR",
+        tumor_options = VARCALL_PARAMS["tnscope"]["tumor"],
         pon = " " if get_pon(config) is None else " ".join(["--pon", get_pon(config)]),
         pcr_model = params.common.pcr_model,
         sentieon_ml_tnscope = config["SENTIEON_TNSCOPE"],

diff --git a/BALSAMIC/snakemake_rules/variant_calling/sentieon_tn_varcall.rule b/BALSAMIC/snakemake_rules/variant_calling/sentieon_tn_varcall.rule
@@ -80,7 +80,6 @@ rule sentieon_TNscope:
     benchmark:
         Path(benchmark_dir, 'sentieon_TNscope_' + config[ "analysis" ][ "case_id" ] + ".tsv").as_posix()
     params:
-        housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
         tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
         tumor = "TUMOR",
         normal = "NORMAL",

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,5 +1,12 @@
+[11.0.1]
+--------
+
+Fixed:
+^^^^^^
+* Incorrect raw `TNscope` VCF delivered https://github.com/Clinical-Genomics/BALSAMIC/pull/1042
+
 [11.0.0]
--------
+--------
 
 Added:
 ^^^^^^