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 |
|---|---|---|---|
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GIAB-v3.0-stratifications-README.md | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | gap_38_1thruY_sorted_merged.bed | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | gaps-PSAY-README_37.txt | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | gaps-PSAY-README_38.txt | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | hg38.README_annotation.md | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | PSA_Y_GRCh38.bed | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | PSA_Y_hg19.bed | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GIAB-stratifications-post-processing-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_stratification_post-processing.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_stratification_post-processing.sh | Open resource |
| Text File | Text | Open resource | |
| Tab Separated Values File | TSV | stratification-file-crosswalk-GRCh37.tsv | Open resource |
| Text File | Text | Open resource | |
| Tab Separated Values File | TSV | stratification-file-crosswalk-GRCh38.tsv | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| PDF File | create_GRCh37_cds_bed.pdf | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | create_GRCh37_cds_bed.Rmd | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-FunctionalRegions-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-FunctionalTechnicallyDifficult-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | MRG_falsely_duplicated.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-GCcontent-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | seqtk_gc.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-GenomeSpecific-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_HG001_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_HG002_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_HG003_v4.2.1_GenomeSpecific_config.yaml | Open resource |
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| Text File | Text | GRCh37_HG004_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_HG005_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_HG006_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_HG007_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | bedtools.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | vcflib.yaml | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
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| Web Resource | Binary | Open resource | |
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| Web Resource | Binary | Open resource | |
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| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Python | findSimpleRegions_quad.py | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | FindSimpleRepeats_v2.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-LowComplexity-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_SimpleRepeat_homopolymer_gt20.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37_SimpleRepeat_imperfecthomoplgt20_slop5.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-mappability-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | make_all_and_notin_beds.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | run_GEM_mappability.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-OtherDifficult-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | merge_difficult_regions_GRCh37_2.01.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-SegDups-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh37-union-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | merge_difficult_regions_GRCh37_2.01.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-ancestry-README.md | Open resource |
| Text File | Text | Open resource | |
| PDF File | create_GRCh38_cds_bed.pdf | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | create_GRCh38_cds_bed.Rmd | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-FunctionalRegions-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-FunctionalTechnicallyDifficult-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | MRG_falsely_duplicated.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-GCcontent-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | grch38_seqtk_gc.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-GenomeSpecific-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG001_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG002_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG003_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG004_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG005_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG006_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_HG007_v4.2.1_GenomeSpecific_config.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | bedtools.yaml | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | vcflib.yaml | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Python | findSimpleRegions_quad.py | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | FindSimpleRepeats_GRCh38_v2.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-LowComplexity-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_SimpleRepeat_homopolymer_gt20.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38_SimpleRepeat_imperfecthomoplgt20_slop5.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-mappability-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | run_GEM_mappability_GRCh38.sh | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | run_GEM_mappability_sort_GRCh38.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-OtherDifficult-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | merge_difficult_regions_GRCh38_2.01.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-SegDups-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GRCh38-union-README.md | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | merge_difficult_regions_GRCh38_2.01.sh | Open resource |
| Text File | Text | Open resource | |
| Web Resource | G-Zipped | v3.0-stratifications-GRCh37.tar.gz | Open resource |
| Text File | Text | Open resource | |
| Web Resource | G-Zipped | v3.0-stratifications-GRCh38.tar.gz | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | human.b37.1_22XY.genome.sorted_noNs_noPSAY_merged.bed | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | human.hg38.1_22XY.genome.sorted_noNs_noPSAY_merged.bed | Open resource |
| Text File | Text | Open resource | |
| Web Resource | Binary | Open resource | |
| Text File | Text | Open resource | |
| Comma Separated Values File | CSV | v3.0-stratfications-info.csv | Open resource |
| Text File | Text | Open resource | |
| Text File | Text | GIAB-stratifications-validation-README.md | Open resource |
| Text File | Text | Open resource | |
| PDF File | v3.0-stratification_validation.pdf | Open resource | |
| Text File | Text | Open resource | |
| Web Resource | Binary | v3.0-stratification_validation.Rmd | Open resource |
| Text File | Text | Open resource | |
| DOI Access for Genome In A Bottle - v3.0 Genome Stratifications | Unknown | Open resource |