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Published May 10, 2023 | Version 1.0.0
Dataset Open

Reference data bundle for PacificBiosciences/wdl-humanwgs

Authors/Creators

  • 1. Pacific Biosciences

Description

Static input files to support alignment, variant calling, filtering, and annotation for human HiFi WGS using the GRCh38 reference.

https://github.com/PacificBiosciences/wdl-humanwgs

static_resources/
├── genes
│   ├── buildGenes
│   ├── ensembl.chrom.tsv
│   ├── ensembl.hgncSymbol.tsv
│   ├── mart_export.txt
│   ├── ncbiGene.ensembl.tsv
│   └── README
├── GRCh38
│   ├── annotation
│   │   ├── GRCh38.oddRegions.bed.gz
│   │   ├── GRCh38.oddRegions.bed.gz.tbi
│   │   ├── GRCh38.repeats.bed.gz
│   │   ├── GRCh38.repeats.bed.gz.tbi
│   │   ├── GRCh38.segdups.bed.gz
│   │   ├── GRCh38.segdups.bed.gz.tbi
│   │   └── README
│   ├── ensembl.GRCh38.101.reformatted.gff3.gz
│   ├── hificnv
│   │   ├── cnv.excluded_regions.common_50.hg38.bed.gz
│   │   ├── cnv.excluded_regions.common_50.hg38.bed.gz.tbi
│   │   ├── female_expected_cn.hg38.bed
│   │   ├── male_expected_cn.hg38.bed
│   │   └── README
│   ├── human_GRCh38_no_alt_analysis_set.chr_lengths.txt
│   ├── human_GRCh38_no_alt_analysis_set.dict
│   ├── human_GRCh38_no_alt_analysis_set.fasta
│   ├── human_GRCh38_no_alt_analysis_set.fasta.fai
│   ├── human_GRCh38_no_alt_analysis_set.ploidy.txt
│   ├── human_GRCh38_no_alt_analysis_set.trf.bed
│   ├── README
│   ├── slivar_gnotate
│   │   ├── add_nhomalt.py
│   │   ├── buildChrX
│   │   ├── buildGnomad
│   │   ├── gnomad.hg38.v3.custom.v1.zip
│   │   ├── hprc.deepvariant.glnexus.hg38.v1.zip
│   │   ├── hprc_samples.txt
│   │   ├── hprc_sex.txt
│   │   └── README
│   ├── sv_pop_vcfs
│   │   ├── EEE_SV-Pop_1.ALL.sites.20181204.vcf.gz
│   │   ├── EEE_SV-Pop_1.ALL.sites.20181204.vcf.gz.tbi
│   │   ├── hprc.GRCh38.pbsv.vcf.gz
│   │   ├── hprc.GRCh38.pbsv.vcf.gz.tbi
│   │   ├── hprc_samples.txt
│   │   ├── nstd166.GRCh38.variant_call.vcf.gz
│   │   ├── nstd166.GRCh38.variant_call.vcf.gz.tbi
│   │   ├── ont_sv_high_confidence_SVs.sorted.vcf.gz
│   │   ├── ont_sv_high_confidence_SVs.sorted.vcf.gz.tbi
│   │   └── README
│   └── trgt
│       ├── human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed
│       └── README
├── hpo
│   ├── buildHpo
│   ├── ensembl.hpoPhenotype.tsv
│   ├── ensembl.inheritance.tsv
│   ├── genes_to_phenotype.txt
│   ├── hpoDagModifications.add.txt
│   ├── hpoDagModifications.remove.txt
│   ├── hpoDag.txt
│   ├── hpoTerms.txt
│   └── README
└── slivar
    ├── clinvar_gene_desc.20221214T183140.txt
    ├── lof_lookup.v2.1.1.txt
    ├── README
    └── slivar-functions.v0.2.8.js

9 directories, 59 files

 

Files

Files (5.3 GB)

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Additional details

References

  • 10.1038/s41588-021-00865-4
  • 10.1016/j.cell.2018.12.019
  • 10.1038/s41586-020-2287-8
  • 10.1038/s41586-020-2308-7