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feat: add snv and sv variant filteration for loqusdb and swegen #1029

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merged 4 commits into from Nov 28, 2022
Merged

feat: add snv and sv variant filteration for loqusdb and swegen #1029

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b2da894
add variant filters
khurrammaqbool Nov 28, 2022
4a77a2a
merge develop
khurrammaqbool Nov 28, 2022
a3e4f0a
add loqusdb and swegen filters
khurrammaqbool Nov 28, 2022
13d8ff1
loqusdb and swegen annotation and filtering for TGA
khurrammaqbool Nov 28, 2022
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31 changes: 15 additions & 16 deletions BALSAMIC/commands/config/case.py
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Open in desktop
Expand Up @@ -243,23 +243,22 @@ def case_config(
with open(reference_config, "r") as f:
reference_dict = json.load(f)["reference"]

if not panel_bed:
variants_observations = {
"clinical_snv_observations": clinical_snv_observations,
"clinical_sv_observations": clinical_sv_observations,
"cancer_all_snv_observations": cancer_all_snv_observations,
"cancer_somatic_snv_observations": cancer_somatic_snv_observations,
"cancer_somatic_sv_observations": cancer_somatic_sv_observations,
"swegen_snv_frequency": swegen_snv,
"swegen_sv_frequency": swegen_sv,
variants_observations = {
"clinical_snv_observations": clinical_snv_observations,
"clinical_sv_observations": clinical_sv_observations,
"cancer_all_snv_observations": cancer_all_snv_observations,
"cancer_somatic_snv_observations": cancer_somatic_snv_observations,
"cancer_somatic_sv_observations": cancer_somatic_sv_observations,
"swegen_snv_frequency": swegen_snv,
"swegen_sv_frequency": swegen_sv,
}
reference_dict.update(
{
observations: path
for observations, path in variants_observations.items()
if path is not None
}
reference_dict.update(
{
observations: path
for observations, path in variants_observations.items()
if path is not None
}
)
)

config_collection_dict = BalsamicConfigModel(
QC={
Expand Down
38 changes: 38 additions & 0 deletions BALSAMIC/constants/variant_filters.py
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Open in desktop
Expand Up @@ -26,6 +26,16 @@
"filter_name": "balsamic_high_pop_freq",
"field": "INFO",
},
"swegen_snv_freq": {
"tag_value": 0.01,
"filter_name": "SWEGENAF",
"field": "INFO",
},
"loqusdb_clinical_snv_freq": {
"tag_value": 0.01,
"filter_name": "Frq",
"field": "INFO",
},
"varcaller_name": "VarDict",
"filter_type": "general",
"analysis_type": "tumor_only",
Expand Down Expand Up @@ -67,8 +77,36 @@
"filter_name": "balsamic_high_strand_oddsratio",
"field": "INFO",
},
"swegen_snv_freq": {
"tag_value": 0.01,
"filter_name": "SWEGENAF",
"field": "INFO",
},
"loqusdb_clinical_snv_freq": {
"tag_value": 0.01,
"filter_name": "Frq",
"field": "INFO",
},
"varcaller_name": "sentieon",
"filter_type": "general",
"analysis_type": "tumor_only",
"description": "General purpose filters used for filtering tnscope and tnhaplotyper",
}

# Configuration for SVDB settings:
SVDB_FILTER_SETTINGS = {
"swegen_sv_freq": {
"tag_value": 0.02,
"filter_name": "SWEGENAF",
"field": "INFO",
},
"loqusdb_clinical_sv_freq": {
"tag_value": 0.02,
"filter_name": "Frq",
"field": "INFO",
},
"varcaller_name": "svdb",
"filter_type": "general",
"analysis_type": "tumor_only,tumor_normal",
"description": "General purpose filters used for filtering svdb merged sv",
}
16 changes: 14 additions & 2 deletions BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_normal.rule
View file
Open in desktop
Expand Up @@ -17,6 +17,7 @@ rule bcftools_filter_vardict_research_tumor_normal:
params:
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
pop_freq = [VARDICT.pop_freq.tag_value, VARDICT.pop_freq.filter_name],
swegen_freq = [VARDICT.swegen_snv_freq.tag_value, VARDICT.swegen_snv_freq.filter_name],
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case_name = '{case_name}',
edit_vcf_script = get_script_path("edit_vcf_info.py"),
variant_caller = "vardict"
Expand All @@ -29,6 +30,7 @@ rule bcftools_filter_vardict_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 filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools view -f PASS -o {output.vcf_pass_vardict}.temp -O z;

tabix -p vcf -f {output.vcf_pass_vardict}.temp;
Expand Down Expand Up @@ -90,6 +92,7 @@ rule bcftools_filter_TNscope_umi_research_tumor_normal:
Path(singularity_image, config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
params:
pop_freq = [SENTIEON_CALLER.pop_freq_umi.tag_value, SENTIEON_CALLER.pop_freq_umi.filter_name],
swegen_freq = [SENTIEON_CALLER.swegen_snv_freq.tag_value, SENTIEON_CALLER.swegen_snv_freq.filter_name],
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
case_name = '{case_name}',
edit_vcf_script = get_script_path("edit_vcf_info.py"),
Expand All @@ -101,8 +104,9 @@ rule bcftools_filter_TNscope_umi_research_tumor_normal:
"adding FOUND_IN tags to the output VCF file for {params.case_name} "
shell:
"""
bcftools view {input.vcf_snv_research} | \
bcftools view -f PASS,triallelic_site --threads {threads} {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 filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;

tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
Expand Down Expand Up @@ -133,6 +137,8 @@ rule bcftools_filter_vardict_clinical_tumor_normal:
params:
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
pop_freq = [VARDICT.pop_freq.tag_value, VARDICT.pop_freq.filter_name],
swegen_freq = [VARDICT.swegen_snv_freq.tag_value, VARDICT.swegen_snv_freq.filter_name],
loqusdb_clinical_freq = [VARDICT.loqusdb_clinical_snv_freq.tag_value, VARDICT.loqusdb_clinical_snv_freq.filter_name],
case_name = '{case_name}',
edit_vcf_script = get_script_path("edit_vcf_info.py"),
variant_caller = "vardict"
Expand All @@ -145,6 +151,8 @@ rule bcftools_filter_vardict_clinical_tumor_normal:
"""
bcftools view {input.vcf_snv_clinical} | \
bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp -O z;

tabix -p vcf -f {output.vcf_pass_vardict}.temp;
Expand Down Expand Up @@ -174,6 +182,8 @@ rule bcftools_filter_TNscope_umi_clinical_tumor_normal:
Path(singularity_image, config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
params:
pop_freq = [SENTIEON_CALLER.pop_freq_umi.tag_value, SENTIEON_CALLER.pop_freq_umi.filter_name],
swegen_freq = [SENTIEON_CALLER.swegen_snv_freq.tag_value, SENTIEON_CALLER.swegen_snv_freq.filter_name],
loqusdb_clinical_freq = [SENTIEON_CALLER.loqusdb_clinical_snv_freq.tag_value, SENTIEON_CALLER.loqusdb_clinical_snv_freq.filter_name],
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
case_name = '{case_name}',
edit_vcf_script = get_script_path("edit_vcf_info.py"),
Expand All @@ -185,8 +195,10 @@ rule bcftools_filter_TNscope_umi_clinical_tumor_normal:
"adding FOUND_IN tags to the output VCF file for {params.case_name} "
shell:
"""
bcftools view {input.vcf_snv_clinical} | \
bcftools view -f PASS,triallelic_site --threads {threads} {input.vcf_snv_clinical} | \
bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;

tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
Expand Down
12 changes: 12 additions & 0 deletions BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule
View file
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Expand Up @@ -17,6 +17,7 @@ rule bcftools_filter_vardict_research_tumor_only:
params:
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
pop_freq = [VARDICT.pop_freq.tag_value, VARDICT.pop_freq.filter_name],
swegen_freq = [VARDICT.swegen_snv_freq.tag_value, VARDICT.swegen_snv_freq.filter_name],
case_name = '{case_name}',
edit_vcf_script = get_script_path("edit_vcf_info.py"),
variant_caller = "vardict"
Expand All @@ -29,6 +30,7 @@ rule bcftools_filter_vardict_research_tumor_only:
"""
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 filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp -O z;

tabix -p vcf -f {output.vcf_pass_vardict}.temp;
Expand Down Expand Up @@ -90,6 +92,7 @@ rule bcftools_filter_TNscope_umi_research_tumor_only:
Path(singularity_image, config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
params:
pop_freq = [SENTIEON_CALLER.pop_freq_umi.tag_value, SENTIEON_CALLER.pop_freq_umi.filter_name],
swegen_freq = [SENTIEON_CALLER.swegen_snv_freq.tag_value, SENTIEON_CALLER.swegen_snv_freq.filter_name],
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
case_name = '{case_name}',
edit_vcf_script = get_script_path("edit_vcf_info.py"),
Expand All @@ -103,6 +106,7 @@ rule bcftools_filter_TNscope_umi_research_tumor_only:
"""
bcftools view {input.vcf_snv_research} | \
bcftools filter --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;

tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
Expand Down Expand Up @@ -133,6 +137,8 @@ rule bcftools_filter_vardict_clinical_tumor_only:
params:
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
pop_freq = [VARDICT.pop_freq.tag_value, VARDICT.pop_freq.filter_name],
swegen_freq = [VARDICT.swegen_snv_freq.tag_value, VARDICT.swegen_snv_freq.filter_name],
loqusdb_clinical_freq = [VARDICT.loqusdb_clinical_snv_freq.tag_value, VARDICT.loqusdb_clinical_snv_freq.filter_name],
case_name = '{case_name}',
edit_vcf_script = get_script_path("edit_vcf_info.py"),
variant_caller = "vardict"
Expand All @@ -145,6 +151,8 @@ rule bcftools_filter_vardict_clinical_tumor_only:
"""
bcftools view {input.vcf_snv_clinical} | \
bcftools filter --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp -O z;

tabix -p vcf -f {output.vcf_pass_vardict}.temp;
Expand Down Expand Up @@ -174,6 +182,8 @@ rule bcftools_filter_TNscope_umi_clinical_tumor_only:
Path(singularity_image,config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
params:
pop_freq=[SENTIEON_CALLER.pop_freq_umi.tag_value, SENTIEON_CALLER.pop_freq_umi.filter_name],
swegen_freq = [SENTIEON_CALLER.swegen_snv_freq.tag_value, SENTIEON_CALLER.swegen_snv_freq.filter_name],
loqusdb_clinical_freq = [SENTIEON_CALLER.loqusdb_clinical_snv_freq.tag_value, SENTIEON_CALLER.loqusdb_clinical_snv_freq.filter_name],
housekeeper_id={"id": config["analysis"]["case_id"], "tags": "clinical"},
case_name='{case_name}',
edit_vcf_script=get_script_path("edit_vcf_info.py"),
Expand All @@ -187,6 +197,8 @@ rule bcftools_filter_TNscope_umi_clinical_tumor_only:
"""
bcftools view {input.vcf_snv_clinical} | \
bcftools filter --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;

tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
Expand Down
14 changes: 12 additions & 2 deletions BALSAMIC/snakemake_rules/annotation/varcaller_sv_filter.rule
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Expand Up @@ -14,14 +14,19 @@ rule bcftools_filter_sv_research:
Path(singularity_image,config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
params:
case_name = "{case_name}",
swegen_freq = [SVDB_FILTERS.swegen_sv_freq.tag_value, SVDB_FILTERS.swegen_sv_freq.filter_name],
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
threads:
get_threads(cluster_config, "bcftools_filter_svdb_research")
message:
"Filtering merged research structural and copy number variants using bcftools for {params.case_name}"
shell:
"""
bcftools view --threads {threads} -f .,PASS,MaxDepth -o {output.vcf_pass_svdb} -O z {input.vcf_sv_research};
bcftools view --threads {threads} -f .,PASS,MaxDepth {input.vcf_sv_research} |\
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f .,PASS,MaxDepth -O z -o {output.vcf_pass_svdb};



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

Expand All @@ -41,14 +46,19 @@ rule bcftools_filter_sv_clinical:
Path(singularity_image,config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
params:
case_name = "{case_name}",
swegen_freq = [SVDB_FILTERS.swegen_sv_freq.tag_value, SVDB_FILTERS.swegen_sv_freq.filter_name],
loqusdb_clinical_freq = [SVDB_FILTERS.loqusdb_clinical_sv_freq.tag_value, SVDB_FILTERS.loqusdb_clinical_sv_freq.filter_name],
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
threads:
get_threads(cluster_config, "bcftools_filter_svdb_clinical")
message:
"Filtering merged clinical structural and copy number variants using bcftools for {params.case_name}"
shell:
"""
bcftools view --threads {threads} -f .,PASS,MaxDepth -o {output.vcf_pass_svdb} -O z {input.vcf_sv_clinical};
bcftools view --threads {threads} -f .,PASS,MaxDepth {input.vcf_sv_clinical} |\
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f .,PASS,MaxDepth -O z -o {output.vcf_pass_svdb};

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

Expand Down
14 changes: 10 additions & 4 deletions BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_normal.rule
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Expand Up @@ -16,6 +16,7 @@ rule bcftools_filter_tnscope_research_tumor_normal:
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],
swegen_freq = [SENTIEON_CALLER.swegen_snv_freq.tag_value, SENTIEON_CALLER.swegen_snv_freq.filter_name],
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "research"},
case_name = '{case_name}'
threads:
Expand All @@ -24,9 +25,10 @@ rule bcftools_filter_tnscope_research_tumor_normal:
"Filtering WGS tumor-normal tnscope annotated research variants using bcftools for {params.case_name}"
shell:
"""
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 --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope} -O z;
bcftools view -f PASS,triallelic_site --threads {threads} {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 filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope} -O z;

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

Expand All @@ -46,6 +48,8 @@ rule bcftools_filter_tnscope_clinical_tumor_normal:
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],
swegen_freq = [SENTIEON_CALLER.swegen_snv_freq.tag_value, SENTIEON_CALLER.swegen_snv_freq.filter_name],
loqusdb_clinical_freq = [SENTIEON_CALLER.loqusdb_clinical_snv_freq.tag_value, SENTIEON_CALLER.loqusdb_clinical_snv_freq.filter_name],
housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
case_name = '{case_name}'
threads:
Expand All @@ -54,8 +58,10 @@ rule bcftools_filter_tnscope_clinical_tumor_normal:
"Filtering WGS tumor-normal tnscope annotated clinical variants using bcftools for {params.case_name}"
shell:
"""
bcftools view {input.vcf_snv_clinical} | \
bcftools view -f PASS,triallelic_site --threads {threads} {input.vcf_snv_clinical} | \
bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope} -O z;

tabix -p vcf -f {output.vcf_pass_tnscope};
Expand Down