| File Path | Source |
|---|---|
nallo/annotation/grch38_clinvar_rename_chromosomes_-v1.0-.txt |
Manually created |
nallo/annotation/grch38_paraphrase_rules.yaml |
Manually created |
shared/genmod_reduced_penetrance.tsv |
Manually created |
nallo/annotation/grch38_strdrop_training_set_260120.json |
Manually created |
nallo/annotation/grch38_trgt_pathogenic_repeats_-v1.0-.txt |
Manually created |
nallo/annotation/grch38_variant_consequences_-v1.0-.txt |
Same as variantconsequences_snv-v1.0-.txt |
nallo/annotation/grch38_vep_112_loftool_scores_-v1.0-.txt |
Downloaded from LoFtool_scores.txt |
nallo/annotation/grch38_vep_112_pli_values_-v1.0-.txt |
Downloaded from pLI_values.txt |
nallo/annotation/grch38_vep_resources_stage_-v1.0-.csv |
Manually created |
nallo/annotation/sites.hg38.vcf.gz |
Downloaded from sites.hg38.vcf.gz, same as hg38.somalier.sites.vcf.gz |
nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini |
Manually created |
nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini |
Manually created |
nallo/region/grch38_chromosomes_split_at_centromeres_-v1.0-.bed |
Manually created |
nallo/region/grch38_hificnv_excluded_regions_common_50_-v1.0-.bed.gz |
Downloaded from cnv.excluded_regions.common_50.hg38.bed.gz |
nallo/region/grch38_hificnv_expected_copynumer_xx_-v1.0-.bed |
Downloaded from expected_cn.hg38.XX.bed |
nallo/region/grch38_hificnv_expected_copynumer_xy_-v1.0-.bed |
Downloaded from expected_cn.hg38.XY.bed |
nallo/region/grch38_methbat_background_292.profile.tsv |
Manually created |
nallo/region/grch38_methbat_promoters_nanoimprint.tsv |
Combined from gencode.v48.promoter_windows.gff3.gz and nanoimprint_regions_hg38.bed |
nallo/region/grch38_par_-v1.0-.bed |
Downloaded from GRCh38_PAR.bed |
nallo/region/hgnc.grch38p14.exons_260122.bed |
Figshare version of scout38 export exons, sorted, added prefix chr, and MT to chrM |
nallo/annotation/grch38_strdrop_training_set_260120.json was created by running strdrop 0.3.1 on TRGT 5.0.0 VCFs run with grch38_trgt_pathogenic_repeats.bed commit 0cd376caa80dd25d4af6ee52155044aeb0aeeee1, from 292 cases sequenced at CG and processed by Nallo.