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resources_hg38.json
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{
"name" : "resources_hg38",
"allosome_file" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/allosome.fai",
"allosomal_contigs" : ["chrX", "chrY"],
"chr_x" : "chrX",
"chr_y" : "chrY",
"autosome_file" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/autosome.fai",
"bin_exclude" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/bin_exclude.hg38.gatkcov.bed.gz",
"bin_exclude_index" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/bin_exclude.hg38.gatkcov.bed.gz.tbi",
"cnmops_exclude_list" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/GRCh38_Nmask.bed",
"contig_ploidy_priors" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/hg38.contig_ploidy_priors_homo_sapiens.tsv",
"copy_number_autosomal_contigs" : 2,
"cytobands" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/cytobands_hg38.bed.gz",
"cytobands_index" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/cytobands_hg38.bed.gz.tbi",
"sd_locs_vcf" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"depth_exclude_list" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/depth_blacklist.sorted.bed.gz",
"depth_exclude_list_index" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/depth_blacklist.sorted.bed.gz.tbi",
"empty_file" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/empty.file",
"exclude_intervals_for_gcnv_filter_intervals" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/hg38.wgs.blacklist.wPAR.bed",
"external_af_population" : ["ALL", "AFR", "AMR", "EAS", "EUR"],
"external_af_ref_bed" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/gnomad_AF/gnomad_v2.1_sv.sites.GRCh38.bed.gz",
"external_af_ref_bed_prefix" : "gnomad_v2.1_sv",
"genome_file" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.genome",
"manta_region_bed" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/primary_contigs_plus_mito.bed.gz",
"manta_region_bed_index" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/primary_contigs_plus_mito.bed.gz.tbi",
"mei_bed" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/mei_hg38.bed.gz",
"melt_std_vcf_header" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/melt_standard_vcf_header.txt",
"noncoding_bed" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/noncoding.sort.hg38.bed",
"pesr_exclude_list" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/PESR.encode.peri_all.repeats.delly.hg38.blacklist.sorted.bed.gz",
"pesr_exclude_list_index" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/PESR.encode.peri_all.repeats.delly.hg38.blacklist.sorted.bed.gz.tbi",
"preprocessed_intervals" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/preprocessed_intervals.interval_list",
"primary_contigs_fai" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/contig.fai",
"primary_contigs_list" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/primary_contigs.list",
"contigs_header": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/hg38_contigs_header.vcf",
"protein_coding_gtf" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/MANE.GRCh38.v1.2.ensembl_genomic.gtf",
"reference_build" : "hg38",
"reference_dict" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"reference_fasta" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"reference_index" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"reference_version" : "38",
"rmsk" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.randomForest_blacklist.withRepMask.bed.gz",
"rmsk_index" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.randomForest_blacklist.withRepMask.bed.gz.tbi",
"segdups" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.SD_gaps_Cen_Tel_Heter_Satellite_lumpy.blacklist.sorted.merged.bed.gz",
"segdups_index" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.SD_gaps_Cen_Tel_Heter_Satellite_lumpy.blacklist.sorted.merged.bed.gz.tbi",
"seed_cutoffs" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/seed_cutoff.txt",
"single_sample_qc_definitions": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/single_sample.qc_definitions.tsv",
"wgd_scoring_mask" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wgd_scoring_mask.hg38.gnomad_v3.bed",
"wham_include_list_bed_file" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wham_whitelist.bed",
"aou_recalibrate_gq_model_file": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/gatk-sv-recalibrator.aou_phase_1.v1.model",
"hgdp_recalibrate_gq_model_file": "gs://gatk-sv-hgdp/mw-sv-concordance-update/hgdp.gq_recalibrator.model",
"recalibrate_gq_genome_tracks": [
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38-RepeatMasker.bed.gz",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38-Segmental-Dups.bed.gz",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38-Simple-Repeats.bed.gz",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38_umap_s100.bed.gz",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38_umap_s24.bed.gz"
],
"recalibrate_gq_genome_track_indexes": [
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38-RepeatMasker.bed.gz.tbi",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38-Segmental-Dups.bed.gz.tbi",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38-Simple-Repeats.bed.gz.tbi",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38_umap_s100.bed.gz.tbi",
"gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38_umap_s24.bed.gz.tbi"
],
"ccdg_abel_site_level_benchmarking_dataset" : ["CCDG_abel", "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/CCDG_Abel"],
"gnomad_v2_collins_sample_level_benchmarking_dataset": ["gnomAD_v2_Collins", "gs://gatk-sv-resources-secure/hg38/v0/sv-resources/resources/v1/gnomAD_v2_Collins_perSample.tar.gz"],
"gnomad_v2_collins_site_level_benchmarking_dataset" : ["gnomAD_v2_Collins", "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/gnomAD_v2_Collins"],
"hgsv_byrska_bishop_sample_level_benchmarking_dataset": ["HGSV_ByrskaBishop", "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/HGSV_ByrskaBishop_GATKSV_perSample.tar.gz"],
"hgsv_byrska_bishop_sample_renaming_tsv": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/rename_sample_ids_HGSV_ByrskaBishop.tsv",
"hgsv_byrska_bishop_site_level_benchmarking_dataset" : ["HGSV_ByrskaBishop", "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/HGSV_ByrskaBishop_GATKSV"],
"hgsv_ebert_sample_level_benchmarking_dataset": ["HGSV_Ebert", "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/HGSV_Ebert_perSample.tar.gz"],
"ssc_belyeu_sample_level_benchmarking_dataset": ["SSC_Belyeu", "gs://gatk-sv-resources-secure/resources/hg38_benchmarking/SSC_Belyeu_perSample.tar.gz"],
"ssc_belyeu_site_level_benchmarking_dataset" : ["SSC_Belyeu", "gs://gatk-sv-resources-secure/resources/hg38_benchmarking/SSC_Belyeu"],
"ssc_sanders_sample_level_benchmarking_dataset": ["SSC_Sanders", "gs://gatk-sv-resources-secure/resources/hg38_benchmarking/SSC_Sanders_perSample.v2.tar.gz"],
"thousand_genomes_site_level_benchmarking_dataset" : ["1000G_Sudmant", "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/1000G_Sudmant"],
"asc_site_level_benchmarking_dataset" : ["ASC_Werling","gs://gatk-sv-resources-secure/resources/hg38_benchmarking/ASC_Werling"],
"hgsv_site_level_benchmarking_dataset" : ["HGSV_Chaisson", "gs://gatk-sv-resources-secure/resources/hg38_benchmarking/HGSV_Chaisson"],
"collins_2017_sample_level_benchmarking_dataset" : ["Collins_2017", "gs://gatk-sv-resources-secure/resources/hg38_benchmarking/Collins_2017_hg38.tar.gz"],
"sanders_2015_sample_level_benchmarking_dataset" : ["Sanders_2015", "gs://gatk-sv-resources-secure/resources/hg38_benchmarking/Sanders_2015_hg38.tar.gz"],
"werling_2018_sample_level_benchmarking_dataset" : ["Werling_2018", "gs://gatk-sv-resources-secure/resources/hg38_benchmarking/Werling_2018_hg38.tar.gz"]
}