├── .gitignore ├── CHANGELOG ├── CHM13v2.0 ├── LowComplexity │ ├── CHM13v2.0-LowComplexity-README.md │ ├── T2T-CHM13v2.0-LowComplexity.ipynb │ └── findSimpleRegions_quad.py ├── OtherDifficult │ ├── CHM13v2.0-OtherDifficult-README.md │ └── T2T-CHM13v2.0-OtherDifficult.ipynb ├── SegmentalDuplications │ ├── CHM13v2.0-SegDups-README.md │ └── T2T-CHM13v2.0-SegDups.ipynb ├── Union │ ├── CHM13v2.0-Union-README.md │ └── T2T-CHM13v2.0-Union.ipynb ├── XY │ ├── CHM13v2.0-XY-README.md │ └── T2T-CHM13v2.0_XY-stratifications.ipynb └── v3.1-CHM13v2.0-all-stratifications.tsv ├── GRCh37 ├── FunctionalRegions │ ├── GRCh37-FunctionalRegions-README.md │ ├── create_GRCh37_cds_bed.Rmd │ └── create_GRCh37_cds_bed.pdf ├── FunctionalTechnicallyDifficult │ ├── GRCh37-FunctionalTechnicallyDifficult-README.md │ └── MRG_falsely_duplicated.sh ├── GCcontent │ ├── GRCh37-GCcontent-README.md │ └── seqtk_gc.sh ├── GenomeSpecific │ ├── GRCh37-GenomeSpecific-README.md │ ├── GRCh37_Generating_v4.1_excluded_beds.ipynb │ ├── GRCh37_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh │ ├── GRCh37_HG002_medical_genes_benchmark_generation.ipynb │ ├── GS-snakemake-pipeline │ │ ├── config │ │ │ ├── GRCh37_HG001_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh37_HG002_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh37_HG003_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh37_HG004_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh37_HG005_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh37_HG006_v4.2.1_GenomeSpecific_config.yaml │ │ │ └── GRCh37_HG007_v4.2.1_GenomeSpecific_config.yaml │ │ └── workflow │ │ │ ├── Snakefile │ │ │ └── envs │ │ │ ├── bedtools.yaml │ │ │ └── vcflib.yaml │ ├── HG001_GRCh37_CNV_exclusion_bed_generation.ipynb │ ├── HG003_GRCh37_CNV_exclusion_bed_generation.ipynb │ ├── HG004_GRCh37_CNV_exclusion_bed_generation.ipynb │ ├── HG005_GRCh37_CNV_exclusion_bed_generation.ipynb │ ├── HG006_GRCh37_CNV_exclusion_bed_generation.ipynb │ └── HG007_GRCh37_CNV_exclusion_bed_generation.ipynb ├── LowComplexity │ ├── GRCh37-LowComplexity-README.md │ ├── GRCh37_LowComplexity.ipynb │ └── findSimpleRegions_quad.py ├── OtherDifficult │ ├── GRCh37-OtherDifficult-README.md │ ├── GRCh37_Generating_v4.1_excluded_beds.ipynb │ └── merge_difficult_regions_GRCh37_2.01.sh ├── SegmentalDuplications │ ├── GRCh37-SegDups-README.md │ ├── GRCh37-SegmentalDuplications.ipynb │ ├── GRCh37_Generating_v4.1_excluded_beds.ipynb │ └── GRCh37_new_chainSelf_and_Segdups.ipynb ├── XY │ ├── GRCh37-XY-README.md │ └── GRCh37_XY.ipynb ├── mappability │ ├── GRCh37-mappability-README.md │ ├── make_all_and_notin_beds.sh │ └── run_GEM_mappability.sh ├── union │ ├── GRCh37-Union.ipynb │ └── GRCh37-union-README.md ├── v3.1-GRCh37-CMRG-stratifications.tsv ├── v3.1-GRCh37-all-stratifications.tsv ├── v3.1-GRCh37-stratifications-all-except-genome-specific-stratifications.tsv └── v3.1-GRCh37-v4.2.1-stratifications.tsv ├── GRCh38 ├── FunctionalRegions │ ├── GRCh38-FunctionalRegions-README.md │ ├── create_GRCh38_cds_bed.Rmd │ └── create_GRCh38_cds_bed.pdf ├── FunctionalTechnicallyDifficult │ ├── GRCh38-FunctionalTechnicallyDifficult-README.md │ └── MRG_falsely_duplicated.sh ├── GCcontent │ ├── GRCh38-GCcontent-README.md │ └── grch38_seqtk_gc.sh ├── GenomeSpecific │ ├── GRCh38-GenomeSpecific-README.md │ ├── GRCh38_Generating_v4.1_excluded_beds.ipynb │ ├── GRCh38_HG002_hifiasmv0.11_ComplexVar_in_TRgt100.sh │ ├── GRCh38_HG002_medical_genes_benchmark_generation.ipynb │ ├── GS-snakemake-pipeline │ │ ├── config │ │ │ ├── GRCh38_HG001_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh38_HG002_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh38_HG003_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh38_HG004_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh38_HG005_v4.2.1_GenomeSpecific_config.yaml │ │ │ ├── GRCh38_HG006_v4.2.1_GenomeSpecific_config.yaml │ │ │ └── GRCh38_HG007_v4.2.1_GenomeSpecific_config.yaml │ │ └── workflow │ │ │ ├── Snakefile │ │ │ └── envs │ │ │ ├── bedtools.yaml │ │ │ └── vcflib.yaml │ ├── HG001_GRCh38_CNV_exclusion_bed_generation.ipynb │ ├── HG003_GRCh38_CNV_exclusion_bed_generation.ipynb │ ├── HG004_GRCh38_CNV_exclusion_bed_generation.ipynb │ ├── HG005_GRCh38_CNV_exclusion_bed_generation.ipynb │ ├── HG006_GRCh38_CNV_exclusion_bed_generation.ipynb │ └── HG007_GRCh38_CNV_exclusion_bed_generation.ipynb ├── LowComplexity │ ├── GRCh38-LowComplexity-README.md │ ├── GRCh38_LowComplexity.ipynb │ └── findSimpleRegions_quad.py ├── OtherDifficult │ ├── GRCh38-OtherDifficult-README.md │ ├── GRCh38_Generating_v4.1_excluded_beds.ipynb │ └── merge_difficult_regions_GRCh38_2.01.sh ├── SegmentalDuplications │ ├── GRCh38-SegDups-README.md │ ├── GRCh38-SegmentalDuplications-v3.1_updated_selfchains.ipynb │ ├── GRCh38_Generating_v4.1_excluded_beds.ipynb │ └── GRCh38_new_chainSelf_and_Segdups.ipynb ├── XY │ ├── GRCh38-XY-README.md │ └── GRCh38_XY.ipynb ├── ancestry │ └── GRCh38-ancestry-README.md ├── mappability │ ├── GRCh38-mappability-README.md │ ├── run_GEM_mappability_GRCh38.sh │ └── run_GEM_mappability_sort_GRCh38.sh ├── union │ ├── GRCh38-Union.ipynb │ ├── GRCh38-union-README.md │ └── merge_difficult_regions_GRCh38_2.01.sh ├── v3.1-GRCh38-CMRG-stratifications.tsv ├── v3.1-GRCh38-all-stratifications.tsv ├── v3.1-GRCh38-stratifications-all-except-genome-specific-stratifications.tsv └── v3.1-GRCh38-v4.2.1-stratifications.tsv ├── README.md ├── post-processing ├── README.md ├── gaps-PSAY-README_37.txt ├── gaps-PSAY-README_38.txt ├── stratification-file-crosswalk-CHM13v2.0.tsv ├── stratification-file-crosswalk-GRCh37.tsv ├── stratification-file-crosswalk-GRCh38.tsv ├── stratification_post-processing.sh └── v3.1_stratification_post-processing.ipynb ├── v3.1-genome-stratifications-md5s.txt └── validation ├── Generate-Genome-Bed-Files-For-Validation.ipynb ├── README.md ├── v3.1-benchmarking-eval-notes.docx ├── v3.1-strat-eval_benchmarking-summary-stats_070622.csv ├── v3.1-stratfication-summary-plots.Rmd ├── v3.1-stratfication-summary-plots.html └── 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