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feat: SVdb merge SV and CNV #886

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merged 13 commits into from
Mar 15, 2022
Merged

feat: SVdb merge SV and CNV #886

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2c09b74
update changelog
khurrammaqbool Mar 10, 2022
b5dc48c
refactor delly, svdb sequencing_type
khurrammaqbool Mar 14, 2022
1fd9d47
refactor varcallers
khurrammaqbool Mar 14, 2022
0c7d2aa
change type for valid_variant_callers
khurrammaqbool Mar 14, 2022
6658601
add sv cnv callers
khurrammaqbool Mar 14, 2022
8105a03
svdb merge sv cnv
khurrammaqbool Mar 14, 2022
922823c
update svdb to 2.5.1
khurrammaqbool Mar 14, 2022
b13d1c5
rename sv_callers to svdb_sv_callers_to_merge_prio
khurrammaqbool Mar 14, 2022
f4b64ba
add get_svdb_input function
khurrammaqbool Mar 14, 2022
f970fa3
lint
khurrammaqbool Mar 14, 2022
8688806
fix CodeFactor suggestion
khurrammaqbool Mar 14, 2022
18b3de9
put input function back in rule
khurrammaqbool Mar 14, 2022
880e860
change var name
khurrammaqbool Mar 14, 2022
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4 changes: 2 additions & 2 deletions BALSAMIC/constants/workflow_params.py
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Expand Up @@ -75,7 +75,7 @@
"mutation": "somatic",
"type": "SV",
"analysis_type": ["paired", "single"],
"sequencing_type": ["wgs", "targeted"],
"sequencing_type": ["targeted", "wgs"],
"workflow_solution": ["BALSAMIC"],
},
"ascat": {
Expand All @@ -89,7 +89,7 @@
"mutation": "somatic",
"type": "SV",
"analysis_type": ["paired", "single"],
"sequencing_type": ["wgs", "targeted"],
"sequencing_type": ["targeted", "wgs"],
"workflow_solution": ["BALSAMIC"],
},
}
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2 changes: 1 addition & 1 deletion BALSAMIC/containers/varcall_py36/varcall_py36.yaml
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Expand Up @@ -9,6 +9,6 @@ dependencies:
- bioconda::gatk=3.8
- bioconda::vardict=2019.06.04=pl526_0
- bioconda::vardict-java=1.7
- bioconda::svdb=2.5.0
- bioconda::svdb=2.5.1
- conda-forge::libiconv
- conda-forge::r-base=3.6.3
16 changes: 11 additions & 5 deletions BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule
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Expand Up @@ -209,8 +209,12 @@ python {params.merge_ascat_output_script} {output.ascat_output_pdf} {input.sampl

rule svdb_merge_tumor_normal:
input:
manta_vcf = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".manta.vcf.gz",
delly_vcf = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.vcf.gz",
vcf = expand(
vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".{caller}.vcf.gz",
caller=somatic_caller_sv) +
expand(
vcf_dir + "CNV.somatic." + config["analysis"]["case_id"] + ".{caller}.vcf.gz",
caller=somatic_caller_cnv)
output:
svdb_vcf = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".svdb.vcf.gz",
namemap = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".svdb.sample_name_map",
Expand All @@ -222,16 +226,18 @@ rule svdb_merge_tumor_normal:
tumor = get_sample_type(config["samples"], "tumor"),
normal = get_sample_type(config["samples"], "normal"),
case_name = config["analysis"]["case_id"],
vcf= lambda wildcards, input:[input[index] + ":" + svdb_callers_prio[index] for index in range(0,len(input))],
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Shouldn't this work?

def construct_vcf(w, i, sv):
  outp=list()
  for index in range(0,len(i)):
     outp.append(f"i[index]:sv[index]")
  return outp

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@hassanfa hassanfa Mar 15, 2022 •
edited
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or maybe not. wildcard is the limiting factor, and can cause an issue. Ignore this :-)

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or maybe not. wildcard is the limiting factor, and can cause an issue. Ignore this :-)

Also, input is not a list and will not iterate in for....

svdb_priority= ",".join(svdb_callers_prio)
threads:
get_threads(cluster_config, "svdb_merge_tumor_normal")
message:
"Merging Manta and Delly results for PASS variants using svdb for sample '{params.case_name}' "
shell:
"""
svdb --merge --no_intra --bnd_distance 5000 --overlap 0.80 \
--vcf {input.manta_vcf}:manta {input.delly_vcf}:delly \
--priority manta,delly | \
bgzip -l 9 -c > {output.svdb_vcf}
--vcf {params.vcf} \
--priority {params.svdb_priority} | \
bgzip -l 9 -c > {output.svdb_vcf};

echo -e \"{params.tumor}\\tTUMOR\\n{params.normal}\\tNORMAL\" > {output.namemap};
"""
17 changes: 11 additions & 6 deletions BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule
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Expand Up @@ -106,8 +106,12 @@ tabix -p vcf -f {output.vcf};

rule svdb_merge_tumor_only:
input:
manta_vcf = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".manta.vcf.gz",
delly_vcf = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.vcf.gz",
vcf = expand(
vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".{caller}.vcf.gz",
caller=somatic_caller_sv) +
expand(
vcf_dir + "CNV.somatic." + config["analysis"]["case_id"] + ".{caller}.vcf.gz",
caller=somatic_caller_cnv)
output:
svdb_vcf = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".svdb.vcf.gz",
namemap = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".svdb.sample_name_map",
Expand All @@ -118,16 +122,17 @@ rule svdb_merge_tumor_only:
params:
tumor = get_sample_type(config["samples"], "tumor"),
case_name = config["analysis"]["case_id"],
vcf= lambda wildcards, input:[input[index] + ":" + svdb_callers_prio[index] for index in range(0,len(input))],
svdb_priority= ",".join(svdb_callers_prio)
threads:
get_threads(cluster_config, "svdb_merge_tumor_only")
message:
"Merging Manta and Delly results for PASS variants using svdb for sample '{params.case_name}' "
shell:
"""
svdb --merge --no_intra --bnd_distance 5000 --overlap 0.80 \
--vcf {input.manta_vcf}:manta {input.delly_vcf}:delly \
--priority manta,delly | \
bgzip -l 9 -c > {output.svdb_vcf}

--vcf {params.vcf} \
--priority {params.svdb_priority} | \
bgzip -l 9 -c > {output.svdb_vcf};
echo -e \"{params.tumor}\\tTUMOR\" > {output.namemap};
"""
6 changes: 3 additions & 3 deletions BALSAMIC/utils/models.py
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Expand Up @@ -176,16 +176,16 @@ def sequencing_type_literal(cls, value) -> str:
class VCFModel(BaseModel):
"""Contains VCF config"""

manta: VarcallerAttribute
cnvkit: VarcallerAttribute
vardict: VarcallerAttribute
tnscope: VarcallerAttribute
dnascope: VarcallerAttribute
tnhaplotyper: VarcallerAttribute
manta_germline: VarcallerAttribute
haplotypecaller: VarcallerAttribute
TNscope_umi: VarcallerAttribute
manta_germline: VarcallerAttribute
manta: VarcallerAttribute
delly: VarcallerAttribute
cnvkit: VarcallerAttribute
ascat: VarcallerAttribute
svdb: VarcallerAttribute

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4 changes: 2 additions & 2 deletions BALSAMIC/utils/rule.py
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Expand Up @@ -75,7 +75,7 @@ def get_variant_callers(
WorkflowRunError if values are not valid
"""

valid_variant_callers = set()
valid_variant_callers = list()
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Changing from list to set might cause redundant entries :-) Make sure you remove them and order it properly now.

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@khurrammaqbool khurrammaqbool Mar 14, 2022 •
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I looked into this and it is not generating redundant entries. The workflow does not show any changes. Using set() generates random order and this has significant impact on the results.

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This can be ambiguous if/when orders change. Just something to keep it in mind.

if mutation_type not in MUTATION_TYPE:
raise WorkflowRunError(f"{mutation_type} is not a valid mutation type.")

Expand All @@ -99,7 +99,7 @@ def get_variant_callers(
and workflow_solution in variant_caller_params.get("workflow_solution")
and sequencing_type in variant_caller_params.get("sequencing_type")
):
valid_variant_callers.add(variant_caller_name)
valid_variant_callers.append(variant_caller_name)
return list(valid_variant_callers)


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18 changes: 18 additions & 0 deletions BALSAMIC/workflows/balsamic.smk
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Expand Up @@ -130,6 +130,8 @@ os.environ['TMPDIR'] = get_result_dir(config)
# Extract variant callers for the workflow
germline_caller = []
somatic_caller = []
somatic_caller_cnv = []
somatic_caller_sv = []
for m in MUTATION_TYPE:
germline_caller_balsamic = get_variant_callers(config=config,
analysis_type=config['analysis']['analysis_type'],
Expand Down Expand Up @@ -170,6 +172,22 @@ for m in MUTATION_TYPE:
mutation_class="somatic")
somatic_caller = somatic_caller + somatic_caller_sentieon_umi + somatic_caller_balsamic + somatic_caller_sentieon

somatic_caller_sv = get_variant_callers(config=config,
analysis_type=config['analysis']['analysis_type'],
workflow_solution="BALSAMIC",
mutation_type="SV",
sequencing_type=config["analysis"]["sequencing_type"],
mutation_class="somatic")

somatic_caller_cnv = get_variant_callers(config=config,
analysis_type=config['analysis']['analysis_type'],
workflow_solution="BALSAMIC",
mutation_type="CNV",
sequencing_type=config["analysis"]["sequencing_type"],
mutation_class="somatic")
somatic_caller_sv.remove("svdb")
svdb_callers_prio = somatic_caller_sv + somatic_caller_cnv

# Collect only snv callers for calculating tmb
somatic_caller_tmb = []
for ws in ["BALSAMIC","Sentieon","Sentieon_umi"]:
Expand Down
2 changes: 1 addition & 1 deletion CHANGELOG.rst
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Expand Up @@ -12,7 +12,7 @@ Added:
* SVdb to WGS workflow #871
* Docker container for vcf2cytosure #858
* SVdb to TGA workflow #871

* SVdb merge SV and CNV #871

Changed:
^^^^^^^^
Expand Down