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References

  • coding_gtf: GENCODE v39 from the gnomAD workspace.
  • dbsnp_vcf (per-contig in data table): Build 156 variants for GRCh38 from dbSNP.
  • dbsnp_vcf_idx (per-contig in data table): Index for dbsnp_vcf.
  • dbvar_vcf (per-contig in data table): Variants for GRCh38 from dbVaR.
  • dbvar_vcf_idx (per-contig in data table): Index for dbvar_vcf.
  • exons_bed: Loci for GRCh38 from the references listed in the SVAN repository.
  • fix_variant_collisions_java: Script for phasing from the DSP Long-Read SV team.
  • genetic_maps_tsv: Maps for GRCh38 from the GLIMPSE references.
  • gnomad_sv_constraint: Genic constraint results for gnomad_sv_vcf.
  • gnomad_sv_vcf: gnomAD V4 structural variants from the gnomAD downloads.
  • gnomad_sv_vcf_idx: Index for gnomad_sv_vcf.
  • gnomad_tr_json: gnomAD V4 tandem repeats from the str-analysis references.
  • gnomad_vcf (per-contig in data table): gnomAD V4 short variants from the gnomAD downloads.
  • gnomad_vcf_idx (per-contig in data table): Indexes for gnomad_vcfs.
  • insilico_cadd_ht: CADD scores for GRCh38 from gnomAD V4.
  • insilico_pangolin_ht: Pangolin scores for GRCh38 from gnomAD V4.
  • insilico_phylop_ht: PhyloP scores for GRCh38 from gnomAD V4.
  • insilico_revel_ht: REVEL scores for GRCh38 from gnomAD V4.
  • insilico_spliceai_ht: SpliceAI scores for GRCh38 from gnomAD V4.
  • mei_catalog: Loci for GRCh38 is a combination of ALU and LINE loci from RepeatMasker and SVA loci from van Bree et al.
  • mei_fa: Sequences for GRCh38 from the SVAN references.
  • mei_fa_indices: BWA and Minimap indices for mei_fa.
  • noncoding_bed: Panel for GRCh38 from the GATK-SV references.
  • par_bed: Panel for GRCh38 from the GATK-SV references.
  • ploidy_bed_female: Panel for GRCh38 from the Kanpig references.
  • ploidy_bed_male: Panel for GRCh38 from the Kanpig references.
  • ref_dict: Sequence dictionary for ref_fa.
  • ref_fa: Sequences for GRCh38 from the PAV references.
  • ref_fai: Index for ref_fa.
  • ref_fa_bwa_indices: BWA indices for ref_fa.
  • ref_fa_indices: BWA and Minimap indices for ref_fa.
  • ref_vep_cache: Cache for v105 from the VEP archives, with the most up-to-date list of these found here.
  • repeat_masker_bed: Loci for GRCh38 from the GATK-SV references.
  • repeats_bed: Loci for GRCh38 from the SVAN references.
  • repeat_catalog_trgt: Catalog for GRCh38 from the TR Catalog references, as used in All of Us Phase.
  • seg_dup_bed: Loci for GRCh38 from the GATK-SV references.
  • simple_repeat_bed: Loci for GRCh38 from the GATK-SV references.
  • seqrepo_tar: Sequence repository v2024-12-20 for GRCh38 from the latest release of seqrepo.
  • truth_hgsvc_ped: Sample pedigree file from the HGSVC FTP server.
  • truth_hgsvc_vcf: HGSVC3 release, combined across the specific VCFs for SNVs, indels and SVs, from the HGSVC FTP server.
  • truth_hgsvc_vcf_idx: Index for truth_hgsvc_vcf.
  • truth_hprc_ped: Sample pedigree file from the HPRC AWS bucket.
  • truth_hprc_vcf: HPRC2 release from the HPRC AWS bucket.
  • truth_hprc_vcf_idx: Index for truth_hprc_vcf.
  • vntr_bed: Loci for GRCh38 from the SVAN references.