genotoscope_local.yaml_

---
### Gene inheritance ###
genes_inheritance_file: "gene_inheritance_patterns_clingen_mhh.xlsx"
thresholds_inheritance_file: "thresholds_inheritance_mode.csv"

### ClinVar ###
clinvar_root: "ClinVar"
clinvar_version: "clinvar_mar_2021"
clinvar_file: "clinvar_20210323.vcf.gz"
clinvar_stars_file: "clinvar_review_stars.tsv"
# ACMG HL expert panel contains variant triggering PM5 using ClinVar entry with one review star
# link: https://www.google.com/url?q=https://erepo.genome.network/evrepo/ui/classification/CA4432734/MONDO:0010134/005&sa=D&source=editors&ust=1617113697097000&usg=AOvVaw1CQYwJirFQyeObmPf9M_ec
min_review_stars: 1


### UniProt ###
# processed UniProt annotation file to contain same number of columns (per bed file)
uniprot_root: "uniprot"
uniprot_version: "uniprot_feb_2021"
uniprot_domains_file: "UP000005640_9606_domain_hg19_15columns.bed"
uniprot_repeat_file: "UP000005640_9606_repeat_hg19_16columns.bed"

### gnomAD ###
gnomAD_version: "gnomAD_v2.1"

### Bed annotations ###
beds_root: "annotation_beds"
# critical regions of proteins
critical_prot_regions_file: "critical_regions_pathogenic_probability.bed"
# critical regions without benign mutation (used in PM1) of proteins
critical_regions_no_benign_file: "critical_regions_pathogenic_probability_no_benign.bed"
# clinical significant exons
clinical_exons_file: "clinical_significant_exons.bed"
# phenotype-relevant (hearing loss) exons
hearing_loss_annot_root: "hearing_loss"
hl_relevant_exons_file: "pheno_relevant_exons_sorted.bed"
# protein regions for PM1 rule as specified by Oza et al. 2018 DOI: 10.1002/humu.23630
hl_pm1_regions_file: "pm1_regions_hl_hg19.bed"

### Hugo genes ###
hugo_genes_file: "hgnc_complete_set_strand.txt"

### pathogenic variants for hearing loss that occur in high AF ###
pheno_high_af_variants_file: "hl_variants.vcf.gz"