diff --git a/cg_hermes/config/raredisease.py b/cg_hermes/config/raredisease.py index 3e3fc49..9e57c7d 100644 --- a/cg_hermes/config/raredisease.py +++ b/cg_hermes/config/raredisease.py @@ -171,6 +171,16 @@ "is_mandatory": False, "used_by": [UsageTags.CG], }, + frozenset(["call_snv_loqusdb", "call_snv_loqusdb"]): { + "tags": [VariantTags.VCF_SNV_LOQUSDB], + "is_mandatory": True, + "used_by": [UsageTags.CG, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE], + }, + frozenset(["call_snv_loqusdb", "call_snv_loqusdb_index"]): { + "tags": [VariantTags.VCF_SNV_LOQUSDB_INDEX], + "is_mandatory": False, + "used_by": [UsageTags.CG, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE], + }, frozenset(["call_sv", "call_sv"]): { "tags": [VariantTags.VCF_SV], "is_mandatory": False, diff --git a/cg_hermes/constants/tags.py b/cg_hermes/constants/tags.py index 38bb3b6..d4896f5 100644 --- a/cg_hermes/constants/tags.py +++ b/cg_hermes/constants/tags.py @@ -87,6 +87,8 @@ class VariantTags(StrEnum): VCF_SNV_GERMLINE_TUMOR: str = "vcf-snv-germline-tumor" VCF_SNV_GERMLINE_TUMOR_INDEX: str = "vcf-snv-germline-tumor-index" VCF_SNV_INDEX: str = "vcf-snv-index" + VCF_SNV_LOQUSDB: str = "vcf-snv-loqusdb" + VCF_SNV_LOQUSDB_INDEX: str = "vcf-snv-loqusdb-index" VCF_SNV_RESEARCH: str = "vcf-snv-research" VCF_SNV_RESEARCH_INDEX: str = "vcf-snv-research-index" VCF_SNV_RESEARCH_UNFILTERED: str = "vcf-snv-research-unfiltered" @@ -155,6 +157,8 @@ def description(self) -> str: self.VCF_SNV_GERMLINE_TUMOR: "SNV germline tumor variants", self.VCF_SNV_GERMLINE_TUMOR_INDEX: "Following index", self.VCF_SNV_INDEX: "Following index", + self.VCF_SNV_LOQUSDB: "Concatenated MT and SNV variants", + self.VCF_SNV_LOQUSDB_INDEX: "Following index", self.VCF_SNV_RESEARCH: "SNV variants from whole genome", self.VCF_SNV_RESEARCH_INDEX: "Following index", self.VCF_STR: "Short tandem repeat variants", diff --git a/docs/raredisease_map.md b/docs/raredisease_map.md index 8569ff9..473d1cb 100644 --- a/docs/raredisease_map.md +++ b/docs/raredisease_map.md @@ -28,6 +28,8 @@ | research_index, annotate_mobile_elements | False | mobile-elements, research, vcf-index | scout, clinical-delivery, long-term-storage | | call_snv | True | vcf-snv | genotype, clinical-delivery, long-term-storage | | call_snv_index, call_snv | False | vcf-snv-index | cg, clinical-delivery, long-term-storage | +| call_snv_loqusdb | True | vcf-snv-loqusdb | cg, clinical-delivery, long-term-storage | +| call_snv_loqusdb_index | True | vcf-snv-loqusdb-index | cg, clinical-delivery, long-term-storage | | call_snv_mt, call_snv | False | vcf-snv, mitochondria | cg | | call_snv, call_snv_mt_index | False | vcf-snv-index, mitochondria | cg | | call_sv | False | vcf-sv | cg, clinical-delivery, long-term-storage | diff --git a/tests/fixtures/raredisease/case_id_deliverables.yaml b/tests/fixtures/raredisease/case_id_deliverables.yaml index 16bc869..8837feb 100644 --- a/tests/fixtures/raredisease/case_id_deliverables.yaml +++ b/tests/fixtures/raredisease/case_id_deliverables.yaml @@ -260,6 +260,16 @@ files: path: PATHTOCASE/call_snv/genome/CASEID_snv.vcf.gz.tbi step: call_snv tag: call_snv_index +- format: vcf + id: CASEID + path: PATHTOCASE/call_snv/concatenated_calls/CASEID_mt_and_nuclear_snvs.vcf.gz + step: call_snv_loqusdb + tag: call_snv_loqusdb +- format: vcf + id: CASEID + path: PATHTOCASE/call_snv/concatenated_calls/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi + step: call_snv_loqusdb + tag: call_snv_loqusdb_index - format: vcf id: CASEID path: PATHTOCASE/call_snv/mitochondria/CASEID_mitochondria.vcf.gz