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updating reference files #107

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92b3b31
updating reference files
jemten Jun 30, 2025
72af746
updating vcfanno toml
jemten Jun 30, 2025
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2 changes: 1 addition & 1 deletion rare-disease/annotation/grch37_svdb_query_dbs_-v1.0-.csv
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Expand Up @@ -2,7 +2,7 @@ filename,in_freq_info_key,in_allele_count_info_key,out_freq_info_key,out_allele_
grch37_svdb_query_decipher_-v1.0.0-.vcf,FRQ,OCC,decipherAF,decipherOCC
grch37_svdb_query_clingen_cgh_benign_-v1.0.0-.vcf,,,clingen_cgh_benign,clingen_cgh_benign
grch37_svdb_query_clingen_ngi_-v1.0.0-.vcf,FRQ,OCC,clingen_ngiAF,clingen_ngiOCC
grch37_loqusdb_sv_variants_export-20250203-.vcf,Frq,Obs,clinical_genomics_loqusFrq,clinical_genomics_loqusObs
grch37_loqusdb_sv_variants_export-20250611-.vcf,Frq,Obs,clinical_genomics_loqusFrq,clinical_genomics_loqusObs
grch37_svdb_query_clingen_cgh_pathogenic_-v2.0.0-.vcf,,,clingen_cgh_pathogenic,clingen_cgh_pathogenic
grch37_gnomad_reformated_sv_-r2.1-.vcf,AF,AC,gnomad_svAF,gnomad_svAC
grch37_mip_sv_svdb_export_-2018-10-09-.vcf,FRQ,OCC,clinical_genomics_mipAF,clinical_genomics_mipOCC
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2 changes: 1 addition & 1 deletion rare-disease/annotation/grch37_svdb_query_dbs_-v1.0-.csv.md5
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@@ -1 +1 @@
9ead473bd130e9e15e6e39dfd8007995 rare-disease/annotation/grch37_svdb_query_dbs_-v1.0-.csv
0bc7dfa25a8080f79fbefb60c935e8d0 rare-disease/annotation/grch37_svdb_query_dbs_-v1.0-.csv
2 changes: 1 addition & 1 deletion rare-disease/annotation/grch37_vcfanno_config_-v1.23-.toml
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Expand Up @@ -15,7 +15,7 @@ ops=["self", "self", "self", "self"]
names=["SWEGENAF", "SWEGENAAC_Hom", "SWEGENAAC_Het", "SWEGENAAC_Hemi"]

[[annotation]]
file="grch37_loqusdb_snv_indel_variants_export-20241004-.vcf.gz"
file="grch37_loqusdb_snv_indel_variants_export-20250611-.vcf.gz"
fields = ["Frq", "Obs", "Hom"]
ops=["self", "self", "self"]
names=["Frq", "Obs", "Hom"]
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2 changes: 1 addition & 1 deletion rare-disease/annotation/grch37_vcfanno_config_-v1.23-.toml.md5
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e2ca3aacc00fce4b33d3988726e72d91 rare-disease/annotation/grch37_vcfanno_config_-v1.23-.toml
e2975200710d3d322f8f7675d5cc9b7c rare-disease/annotation/grch37_vcfanno_config_-v1.23-.toml
4 changes: 2 additions & 2 deletions rare-disease/annotation/grch37_vcfanno_resources_-v1.0-.txt
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Expand Up @@ -8,7 +8,7 @@ grch37_gnomad_genomes_mt_-r3.1-.vcf.gz
grch37_gnomad_genomes_mt_-r3.1-.vcf.gz.tbi
grch37_gnomad_reformated_-r2.1.1-.vcf.gz
grch37_gnomad_reformated_-r2.1.1-.vcf.gz.tbi
grch37_loqusdb_snv_indel_variants_export-20250203-.vcf.gz
grch37_loqusdb_snv_indel_variants_export-20250203-.vcf.gz.tbi
grch37_loqusdb_snv_indel_variants_export-20250611-.vcf.gz
grch37_loqusdb_snv_indel_variants_export-20250611-.vcf.gz.tbi
grch37_spidex_public_noncommercial_-v1.1-.tsv.gz
grch37_spidex_public_noncommercial_-v1.1-.tsv.gz.tbi
2 changes: 1 addition & 1 deletion rare-disease/annotation/grch37_vcfanno_resources_-v1.0-.txt.md5
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c18ac0f5b77c15037bfec7f0d35501bf rare-disease/annotation/grch37_vcfanno_resources_-v1.0-.txt
a94667756c88f9b2058e4702fd2ed040 rare-disease/annotation/grch37_vcfanno_resources_-v1.0-.txt
4 changes: 2 additions & 2 deletions rare-disease/annotation/grch37_vep110_resources_-v1.0-.csv
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@@ -1,7 +1,7 @@
vep_files
gnomad_pli_per_gene_-r2.1.1-.txt
grch37_clinvar_reformatted_-20250202-.vcf.gz
grch37_clinvar_reformatted_-20250202-.vcf.gz.tbi
grch37_clinvar_reformatted_-20250608-.vcf.gz
grch37_clinvar_reformatted_-20250608-.vcf.gz.tbi
grch37_dbnsfp_-v3.5a-.txt.gz
grch37_dbnsfp_-v3.5a-.txt.gz.tbi
grch37_genomic_superdups_reformated_-20181009-.bed.gz
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2 changes: 1 addition & 1 deletion rare-disease/annotation/grch37_vep110_resources_-v1.0-.csv.md5
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5b08a4963d0e3060ab673de6d0b96c44 rare-disease/annotation/grch37_vep110_resources_-v1.0-.csv
cbace97ee9e6bcffde8e7f064a95d527 rare-disease/annotation/grch37_vep110_resources_-v1.0-.csv