refactor: Disable tnhaplotyper for TN WGS

BALSAMIC/config/cluster.json

@@ -100,10 +100,6 @@
 		"time": "24:00:00",
 		"n": 24
 	},
-	"sentieon_TN_corealign": {
-		"time": "24:00:00",
-		"n": 24
-	},
 	"sentieon_TNhaplotyper": {
 		"time": "24:00:00",
 		"n": 24

BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_normal.rule

@@ -45,38 +45,3 @@ tabix -p vcf -f {output.vcf_pass_tnscope};
 
 bcftools +counts {output.vcf_pass_tnscope} > {output.bcftools_counts};
     """
-
-
-rule bcftools_filter_tnhaplotyper_tumor_normal:
-  input:
-    vcf = vep_dir + "{var_type}.somatic.{case_name}.tnhaplotyper.all.vcf.gz",
-    wgs_calling_file = config["reference"]["wgs_calling_interval"]
-  output:
-    vcf_filtered = vep_dir + "{var_type}.somatic.{case_name}.tnhaplotyper.all.filtered.vcf.gz",
-    vcf_pass_tnhaplotyper = vep_dir + "{var_type}.somatic.{case_name}.tnhaplotyper.all.filtered.pass.vcf.gz",
-  benchmark:
-    Path(benchmark_dir, 'bcftools_filter_tnhaplotyper_tumor_normal_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
-  singularity:
-    Path(singularity_image, config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
-  params:
-    pop_freq = [SENTIEON_CALLER.pop_freq.tag_value, SENTIEON_CALLER.pop_freq.filter_name],
-    case_name = '{case_name}'
-  threads: 
-    get_threads(cluster_config, 'bcftools_filter_tnhaplotyper_tumor_normal')
-  message:
-    "Filtering WGS tumor-normal tnhaplotyper annotated variants using bcftools for {params.case_name}"
-  shell:
-    """
-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} \
-| bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' \
-| bcftools view -o {output.vcf_filtered} -O z;
-
-tabix -p vcf -f {output.vcf_filtered};
-
-bcftools view -f PASS --threads {threads} -O z -o {output.vcf_pass_tnhaplotyper} {output.vcf_filtered}
-
-tabix -p vcf -f {output.vcf_pass_tnhaplotyper}
-
-    """

BALSAMIC/snakemake_rules/variant_calling/sentieon_tn_varcall.rule

@@ -64,95 +64,6 @@ rm -rf {params.tmpdir};
         """
 
 
-rule sentieon_TN_corealign:
-    input:
-        ref = config["reference"]["reference_genome"],
-        bamT = expand(bam_dir + "tumor.merged.bam"),
-        bamN = expand(bam_dir + "normal.merged.bam"),
-        recalT = expand(bam_dir + "tumor.merged.recal_data.table"),
-        recalN = expand(bam_dir + "normal.merged.recal_data.table"),
-        mills = config["reference"]["mills_1kg"],
-        indel_1kg = config["reference"]["1kg_known_indel"],
-    output:
-        bam = bam_dir + config["analysis"]["case_id"] + ".corealign.bam"
-    benchmark:
-        Path(benchmark_dir, 'sentieon_TN_corealign_' + config[ "analysis" ][ "case_id" ] + ".tsv").as_posix()
-    params:
-        tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
-        sentieon_exec = config["SENTIEON_EXEC"],
-        sentieon_lic = config["SENTIEON_LICENSE"],
-        case_name = config["analysis"]["case_id"]
-    threads:
-        get_threads(cluster_config, 'sentieon_TN_corealign')
-    message:
-        ("Perform local realignment around indels on the bam files"
-         " using Sentieon tools for sample {params.case_name}")
-    shell:
-        """
-mkdir -p {params.tmpdir};
-export TMPDIR={params.tmpdir};
-export SENTIEON_TMPDIR={params.tmpdir};
-export SENTIEON_LICENSE={params.sentieon_lic};
-
-{params.sentieon_exec} driver \
--r {input.ref} \
--t {threads} \
--i {input.bamT} \
--i {input.bamN} \
--q {input.recalT} \
--q {input.recalN} \
---algo Realigner \
--k {input.mills} \
--k {input.indel_1kg} {output.bam}
-
-rm -rf {params.tmpdir};
-        """
-
-
-rule sentieon_TNhaplotyper:
-    input:
-        bam = bam_dir + config["analysis"]["case_id"] + ".corealign.bam",
-        ref = config["reference"]["reference_genome"],
-        dbsnp = config["reference"]["dbsnp"],
-    output:
-        vcf = vcf_dir + "SNV.somatic." + config["analysis"]["case_id"] + ".tnhaplotyper.vcf.gz",
-        namemap = vcf_dir + "SNV.somatic." + config["analysis"]["case_id"] + ".tnhaplotyper.sample_name_map",
-    benchmark:
-        Path(benchmark_dir, 'sentieon_TNhaplotyper_' + config[ "analysis" ][ "case_id" ] + ".tsv").as_posix()
-    params:
-        tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
-        tumor = "TUMOR", 
-        normal = "NORMAL",
-        pcr_model = params.common.pcr_model,
-        sentieon_exec = config["SENTIEON_EXEC"],
-        sentieon_lic = config["SENTIEON_LICENSE"],
-        case_name = config["analysis"]["case_id"]
-    threads:
-        get_threads(cluster_config, 'sentieon_TNhaplotyper')
-    message:
-        "Calling SNV variants using Sentieon TNhaplotyper for sample {params.case_name}"
-    shell:
-        """
-mkdir -p {params.tmpdir};
-export TMPDIR={params.tmpdir};
-export SENTIEON_TMPDIR={params.tmpdir};
-export SENTIEON_LICENSE={params.sentieon_lic};
-
-{params.sentieon_exec} driver \
--r {input.ref} \
--t {threads} \
--i {input.bam} \
---algo TNhaplotyper \
---tumor_sample {params.tumor} \
---normal_sample {params.normal} \
---pcr_indel_mode {params.pcr_model} \
---dbsnp {input.dbsnp} {output.vcf};
-
-echo -e \"{params.tumor}\\tTUMOR\\n{params.normal}\\tNORMAL\" > {output.namemap};
-rm -rf {params.tmpdir};
-        """
-
-
 rule sentieon_TNscope:
     input:
         ref = config["reference"]["reference_genome"],
@@ -173,8 +84,8 @@ rule sentieon_TNscope:
         tumor = "TUMOR",
         normal = "NORMAL",
         pcr_model = params.common.pcr_model,
-        tumor_options = VARCALL_PARAMS["tnscope"]["tumor"], 
-        normal_options = VARCALL_PARAMS["tnscope"]["normal"], 
+        tumor_options = VARCALL_PARAMS["tnscope"]["tumor"],
+        normal_options = VARCALL_PARAMS["tnscope"]["normal"],
         sentieon_ml_tnscope = config["SENTIEON_TNSCOPE"],
         sentieon_exec = config["SENTIEON_EXEC"],
         sentieon_lic = config["SENTIEON_LICENSE"],

BALSAMIC/workflows/balsamic.smk

@@ -218,6 +218,12 @@ for ws in ["BALSAMIC","Sentieon","Sentieon_umi"]:
                                            mutation_class="somatic")
     somatic_caller_tmb +=  somatic_caller_snv
 
+
+# Remove TNhaplotyer for WGS-TN analysis
+if config["analysis"]["sequencing_type"] == "wgs" and config['analysis']['analysis_type'] == "paired":
+    somatic_caller.remove("tnhaplotyper")
+    somatic_caller_tmb.remove("tnhaplotyper")
+
 # Remove variant callers from list of callers
 if "disable_variant_caller" in config:
     variant_callers_to_remove = config["disable_variant_caller"].split(",")

CHANGELOG.rst

@@ -17,6 +17,7 @@ Removed
 ^^^^^^^
 
 * case ID from the PON `.cnn` output file https://github.com/Clinical-Genomics/BALSAMIC/pull/983
+* TNhaplotyper for paired WGS analysis https://github.com/Clinical-Genomics/BALSAMIC/pull/988
 
 [10.0.2]
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