Genome In A Bottle - v3.0 Genome Stratifications

Description

These v3.0 stratification BED files from the Global Alliance for Genomic Health (GA4GH) Benchmarking Team, the Genome in a Bottle Consortium and the Telomere-to-Telomere Consortium are intended as a standard resource of BED files for use in stratifying true positive, false positive, and false negative variant calls in challenging and targeted regions of the the genome. v3.0 stratifications contain new and revised stratification files and replace v2.0 stratifications.

Resources

Name Format Description Link
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG005_GRCh37_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/FindSimpleRepeats_v2.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/GRCh37_SimpleRepeat_homopolymer_gt20.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalRegions/create_GRCh38_cds_bed.pdf.sha256
47 GRCh38-FunctionalTechnicallyDifficult-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalTechnicallyDifficult/GRCh38-FunctionalTechnicallyDifficult-README.md
47 GRCh38_HG005_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG005_v4.2.1_GenomeSpecific_config.yaml
47 GRCh38_HG007_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG007_v4.2.1_GenomeSpecific_config.yaml
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/workflow/Snakefile
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/vcflib.yaml.sha256
47 GRCh38-SegDups-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/SegmentalDuplications/GRCh38-SegDups-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/stratification-file-crosswalk-GRCh37.tsv.sha256
47 run_GEM_mappability_sort_GRCh38.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/mappability/run_GEM_mappability_sort_GRCh38.sh
49 stratification-file-crosswalk-GRCh37.tsv https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/stratification-file-crosswalk-GRCh37.tsv
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38_Generating_v4.1_excluded_beds.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG007_v4.2.1_GenomeSpecific_config.yaml.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/mappability/run_GEM_mappability_sort_GRCh38.sh.sha256
19 v3.0-stratifications-GRCh37.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2499/v3.0-stratifications-GRCh37.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/GRCh37_stratification_post-processing.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/GRCh38_stratification_post-processing.sh.sha256
5 PSA_Y_GRCh38.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/PSA_Y_GRCh38.bed
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/PSA_Y_GRCh38.bed.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/PSA_Y_hg19.bed.sha256
5 gap_38_1thruY_sorted_merged.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/gap_38_1thruY_sorted_merged.bed
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/gap_38_1thruY_sorted_merged.bed.sha256
47 gaps-PSAY-README_37.txt https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/gaps-PSAY-README_37.txt
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/gaps-PSAY-README_37.txt.sha256
49 stratification-file-crosswalk-GRCh38.tsv https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/stratification-file-crosswalk-GRCh38.tsv
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/v2.01.00_stratification_post-processing.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/v2.01.00_stratification_post-processing.ipynb.sha256
5 create_GRCh37_cds_bed.Rmd https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalRegions/create_GRCh37_cds_bed.Rmd
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalRegions/create_GRCh37_cds_bed.Rmd.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalTechnicallyDifficult/GRCh37-FunctionalTechnicallyDifficult-README.md.sha256
47 MRG_falsely_duplicated.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalTechnicallyDifficult/MRG_falsely_duplicated.sh
47 GRCh37-GCcontent-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GCcontent/GRCh37-GCcontent-README.md
47 seqtk_gc.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GCcontent/seqtk_gc.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GCcontent/seqtk_gc.sh.sha256
47 GRCh37-GenomeSpecific-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37-GenomeSpecific-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37_Generating_v4.1_excluded_beds.ipynb.sha256
47 GRCh37_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh
47 bedtools.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/bedtools.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/bedtools.yaml.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG001_GRCh37_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG001_GRCh37_CNV_exclusion_bed_generation.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG003_GRCh37_CNV_exclusion_bed_generation.ipynb.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG004_GRCh37_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG004_GRCh37_CNV_exclusion_bed_generation.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG005_GRCh37_CNV_exclusion_bed_generation.ipynb.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG006_GRCh37_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG006_GRCh37_CNV_exclusion_bed_generation.ipynb.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG007_GRCh37_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG007_GRCh37_CNV_exclusion_bed_generation.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG001_v4.2.1_GenomeSpecific_config.yaml.sha256
47 GRCh37_HG002_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG002_v4.2.1_GenomeSpecific_config.yaml
47 GRCh37_SimpleRepeat_imperfecthomoplgt20_slop5.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/GRCh37_SimpleRepeat_imperfecthomoplgt20_slop5.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/GRCh37_SimpleRepeat_imperfecthomoplgt20_slop5.sh.sha256
37 findSimpleRegions_quad.py https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/findSimpleRegions_quad.py
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/findSimpleRegions_quad.py.sha256
47 GRCh37-OtherDifficult-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/OtherDifficult/GRCh37-OtherDifficult-README.md
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/OtherDifficult/GRCh37_Generating_v4.1_excluded_beds.ipynb
47 merge_difficult_regions_GRCh37_2.01.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/OtherDifficult/merge_difficult_regions_GRCh37_2.01.sh
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/CHANGELOG
47 GIAB-v3.0-stratifications-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/GIAB-v3.0-stratifications-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/GIAB-v3.0-stratifications-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG003_v4.2.1_GenomeSpecific_config.yaml.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG004_v4.2.1_GenomeSpecific_config.yaml.sha256
47 GIAB-stratifications-post-processing-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/GIAB-stratifications-post-processing-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/GIAB-stratifications-post-processing-README.md.sha256
5 create_GRCh38_cds_bed.Rmd https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalRegions/create_GRCh38_cds_bed.Rmd
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38-GenomeSpecific-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38_HG002_medical_genes_benchmark_generation.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG001_v4.2.1_GenomeSpecific_config.yaml.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG002_v4.2.1_GenomeSpecific_config.yaml.sha256
47 GRCh38_HG003_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG003_v4.2.1_GenomeSpecific_config.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG003_v4.2.1_GenomeSpecific_config.yaml.sha256
47 GRCh38_HG004_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG004_v4.2.1_GenomeSpecific_config.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/OtherDifficult/merge_difficult_regions_GRCh37_2.01.sh.sha256
47 GRCh37-SegDups-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/SegmentalDuplications/GRCh37-SegDups-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/SegmentalDuplications/GRCh37-SegDups-README.md.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/SegmentalDuplications/GRCh37_Generating_v4.1_excluded_beds.ipynb
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/SegmentalDuplications/GRCh37_new_chainSelf_and_Segdups.ipynb
47 GRCh37-mappability-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/mappability/GRCh37-mappability-README.md
47 make_all_and_notin_beds.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/mappability/make_all_and_notin_beds.sh
47 run_GEM_mappability.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/mappability/run_GEM_mappability.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/mappability/run_GEM_mappability.sh.sha256
47 GRCh37-union-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/union/GRCh37-union-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/union/GRCh37-union-README.md.sha256
47 merge_difficult_regions_GRCh37_2.01.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/union/merge_difficult_regions_GRCh37_2.01.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/union/merge_difficult_regions_GRCh37_2.01.sh.sha256
47 GRCh38-FunctionalRegions-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalRegions/GRCh38-FunctionalRegions-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/workflow/Snakefile.sha256
47 bedtools.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/bedtools.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/bedtools.yaml.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG001_GRCh38_CNV_exclusion_bed_generation.ipynb.sha256
47 GRCh38-LowComplexity-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/GRCh38-LowComplexity-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/GRCh38-LowComplexity-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/GRCh38_SimpleRepeat_homopolymer_gt20.sh.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG004_GRCh38_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG004_GRCh38_CNV_exclusion_bed_generation.ipynb.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG005_GRCh38_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG007_GRCh38_CNV_exclusion_bed_generation.ipynb.sha256
47 FindSimpleRepeats_GRCh38_v2.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/FindSimpleRepeats_GRCh38_v2.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/GRCh38_SimpleRepeat_imperfecthomoplgt20_slop5.sh.sha256
37 findSimpleRegions_quad.py https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/findSimpleRegions_quad.py
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/findSimpleRegions_quad.py.sha256
47 GRCh38-OtherDifficult-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/OtherDifficult/GRCh38-OtherDifficult-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/OtherDifficult/GRCh38-OtherDifficult-README.md.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/OtherDifficult/GRCh38_Generating_v4.1_excluded_beds.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/OtherDifficult/GRCh38_Generating_v4.1_excluded_beds.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/SegmentalDuplications/GRCh38_Generating_v4.1_excluded_beds.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/v3.0-stratifications-GRCh37.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/v3.0-stratifications-GRCh38.tar.gz.sha256
47 GIAB-stratifications-validation-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/GIAB-stratifications-validation-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/GIAB-stratifications-validation-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/README_for_genome_bed_files.sha256
5 human.b37.1_22XY.genome.sorted_noNs_noPSAY_merged.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/human.b37.1_22XY.genome.sorted_noNs_noPSAY_merged.bed
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/human.hg38.1_22XY.genome.sorted_noNs_noPSAY_merged.bed.sha256
33 v3.0-stratification_validation.pdf https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/v3.0-stratification_validation.pdf
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/v3.0-stratification_validation.pdf.sha256
0 https://doi.org/10.18434/mds2-2499
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalRegions/create_GRCh37_cds_bed.pdf.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG005_v4.2.1_GenomeSpecific_config.yaml.sha256
47 hg38.README_annotation.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/hg38.README_annotation.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37-GenomeSpecific-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37_HG002_medical_genes_benchmark_generation.ipynb.sha256
47 FindSimpleRepeats_v2.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/FindSimpleRepeats_v2.sh
33 create_GRCh38_cds_bed.pdf https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalRegions/create_GRCh38_cds_bed.pdf
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalTechnicallyDifficult/GRCh38-FunctionalTechnicallyDifficult-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38_Generating_v4.1_excluded_beds.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG004_v4.2.1_GenomeSpecific_config.yaml.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/mappability/GRCh37-mappability-README.md.sha256
47 vcflib.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/vcflib.yaml
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG003_GRCh38_CNV_exclusion_bed_generation.ipynb
47 merge_difficult_regions_GRCh38_2.01.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/OtherDifficult/merge_difficult_regions_GRCh38_2.01.sh
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/README_for_genome_bed_files
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/human.b37.1_22XY.genome.sorted_noNs_noPSAY_merged.bed.sha256
47 GRCh37_HG005_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG005_v4.2.1_GenomeSpecific_config.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GCcontent/GRCh38-GCcontent-README.md.sha256
47 grch38_seqtk_gc.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GCcontent/grch38_seqtk_gc.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GCcontent/grch38_seqtk_gc.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/mappability/make_all_and_notin_beds.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalRegions/GRCh37-FunctionalRegions-README.md.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37_Generating_v4.1_excluded_beds.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/OtherDifficult/GRCh37-OtherDifficult-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/mappability/GRCh38-mappability-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG005_GRCh38_CNV_exclusion_bed_generation.ipynb.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG006_GRCh38_CNV_exclusion_bed_generation.ipynb
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG007_GRCh38_CNV_exclusion_bed_generation.ipynb
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/SegmentalDuplications/GRCh38_new_chainSelf_and_Segdups.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/SegmentalDuplications/GRCh38_new_chainSelf_and_Segdups.ipynb.sha256
47 GRCh38-ancestry-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/ancestry/GRCh38-ancestry-README.md
47 GRCh38-mappability-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/mappability/GRCh38-mappability-README.md
47 GRCh37-FunctionalTechnicallyDifficult-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalTechnicallyDifficult/GRCh37-FunctionalTechnicallyDifficult-README.md
47 GRCh37_SimpleRepeat_homopolymer_gt20.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/GRCh37_SimpleRepeat_homopolymer_gt20.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/CHANGELOG.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38_HG002_medical_genes_benchmark_generation.ipynb
47 run_GEM_mappability_GRCh38.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/mappability/run_GEM_mappability_GRCh38.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/v3.0-stratification_validation.Rmd.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GCcontent/GRCh37-GCcontent-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG006_v4.2.1_GenomeSpecific_config.yaml.sha256
47 GRCh38-GenomeSpecific-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38-GenomeSpecific-README.md
47 merge_difficult_regions_GRCh38_2.01.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/union/merge_difficult_regions_GRCh38_2.01.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/v3.0-stratfications-info.csv.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG001_GRCh38_CNV_exclusion_bed_generation.ipynb
33 create_GRCh37_cds_bed.pdf https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalRegions/create_GRCh37_cds_bed.pdf
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/workflow/Snakefile.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/GRCh37-LowComplexity-README.md.sha256
47 GRCh38_SimpleRepeat_imperfecthomoplgt20_slop5.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/GRCh38_SimpleRepeat_imperfecthomoplgt20_slop5.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/gaps-PSAY-README_38.txt.sha256
47 GRCh38-GCcontent-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GCcontent/GRCh38-GCcontent-README.md
47 GRCh38_stratification_post-processing.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/GRCh38_stratification_post-processing.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/hg38.README_annotation.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/stratification-file-crosswalk-GRCh38.tsv.sha256
47 GRCh37-FunctionalRegions-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalRegions/GRCh37-FunctionalRegions-README.md
47 GRCh37_HG001_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG001_v4.2.1_GenomeSpecific_config.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG007_v4.2.1_GenomeSpecific_config.yaml.sha256
47 GRCh37_HG003_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG003_v4.2.1_GenomeSpecific_config.yaml
47 GRCh37-LowComplexity-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/LowComplexity/GRCh37-LowComplexity-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG005_v4.2.1_GenomeSpecific_config.yaml.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalRegions/create_GRCh38_cds_bed.Rmd.sha256
47 MRG_falsely_duplicated.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalTechnicallyDifficult/MRG_falsely_duplicated.sh
47 GRCh38_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GRCh38_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh
47 GRCh38_HG006_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG006_v4.2.1_GenomeSpecific_config.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG006_v4.2.1_GenomeSpecific_config.yaml.sha256
47 GRCh38_SimpleRepeat_homopolymer_gt20.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/GRCh38_SimpleRepeat_homopolymer_gt20.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/OtherDifficult/merge_difficult_regions_GRCh38_2.01.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/SegmentalDuplications/GRCh38-SegDups-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/mappability/run_GEM_mappability_GRCh38.sh.sha256
47 GRCh38-union-README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/union/GRCh38-union-README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/union/GRCh38-union-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/union/merge_difficult_regions_GRCh38_2.01.sh.sha256
5 v3.0-stratification_validation.Rmd https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/v3.0-stratification_validation.Rmd
5 PSA_Y_hg19.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/PSA_Y_hg19.bed
47 vcflib.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/vcflib.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/workflow/envs/vcflib.yaml.sha256
47 GRCh37_HG006_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG006_v4.2.1_GenomeSpecific_config.yaml
47 GRCh38_HG001_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG001_v4.2.1_GenomeSpecific_config.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/SegmentalDuplications/GRCh37_Generating_v4.1_excluded_beds.ipynb.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37_HG002_medical_genes_benchmark_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/LowComplexity/FindSimpleRepeats_GRCh38_v2.sh.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/SegmentalDuplications/GRCh38_Generating_v4.1_excluded_beds.ipynb
5 human.hg38.1_22XY.genome.sorted_noNs_noPSAY_merged.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/human.hg38.1_22XY.genome.sorted_noNs_noPSAY_merged.bed
47 GRCh37_HG004_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG004_v4.2.1_GenomeSpecific_config.yaml
47 gaps-PSAY-README_38.txt https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/dependency-files/gaps-PSAY-README_38.txt
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GRCh37_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh.sha256
47 GRCh37_HG007_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG007_v4.2.1_GenomeSpecific_config.yaml
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/workflow/Snakefile
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/HG003_GRCh37_CNV_exclusion_bed_generation.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/GenomeSpecific/GS-snakemake-pipeline/config/GRCh37_HG002_v4.2.1_GenomeSpecific_config.yaml.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalTechnicallyDifficult/MRG_falsely_duplicated.sh.sha256
47 GRCh38_HG002_v4.2.1_GenomeSpecific_config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/GS-snakemake-pipeline/config/GRCh38_HG002_v4.2.1_GenomeSpecific_config.yaml
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/SegmentalDuplications/GRCh37_new_chainSelf_and_Segdups.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/FunctionalRegions/GRCh38-FunctionalRegions-README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG003_GRCh38_CNV_exclusion_bed_generation.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/GenomeSpecific/HG006_GRCh38_CNV_exclusion_bed_generation.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh38/ancestry/GRCh38-ancestry-README.md.sha256
19 v3.0-stratifications-GRCh38.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2499/v3.0-stratifications-GRCh38.tar.gz
8 v3.0-stratfications-info.csv https://data.nist.gov/od/ds/ark:/88434/mds2-2499/validation/dependency-files/v3.0-stratfications-info.csv
47 GRCh37_stratification_post-processing.sh https://data.nist.gov/od/ds/ark:/88434/mds2-2499/post-processing/GRCh37_stratification_post-processing.sh
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/FunctionalTechnicallyDifficult/MRG_falsely_duplicated.sh.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2499/stratification-generation/GRCh37/OtherDifficult/GRCh37_Generating_v4.1_excluded_beds.ipynb.sha256

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