├── .gitignore ├── LICENSE ├── README.md ├── benchmark ├── .gitignore ├── GIABTR_benchmark.6.26 │ └── README.md ├── README.md ├── inputs │ ├── GRCh38.chrX.PAR.bed │ ├── GRCh38_1kg_mainchrs.genome_bedtools.bed │ └── replicate_curated_states.txt └── scripts │ ├── allele_delta.py │ ├── consolidate_refine_regions.py │ ├── covered_regions.sh │ ├── hg002_subsets.sh │ ├── makeTiers.sh │ ├── make_tiers.py │ ├── run_repl_bench.sh │ ├── single_sample_covered_regions.sh │ └── test_makeTiers.sh ├── benchmarking ├── .gitignore ├── README.md ├── bed_region_cluster │ ├── .gitignore │ ├── README.md │ └── make_upset.py ├── notebooks │ ├── .gitignore │ ├── AdvancedReporting.ipynb │ ├── VariantBenchmarking.ipynb │ └── VariantsPerRegion.ipynb ├── scripts │ ├── bench_region_counter.sh │ ├── consolidate_summary.py │ ├── fixer.sh │ ├── json_to_table.py │ ├── mk_bench.sh │ ├── mkdf4rtg.py │ ├── per_region_varcount.sh │ ├── rehom.py │ └── trgt_statelen.py └── submit_refine.sh ├── codis ├── AllautosomeChrY.bed ├── README.md ├── STR_Grch38_autosomes.bed ├── STR_Grch38_sexchr.bed ├── codis_phab_autosomes │ ├── chr10:129294243-129294295 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr11:2171087-2171115 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr12:12297019-12297095 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr12:5983976-5984044 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr13:82148024-82148068 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr15:96831014-96831039 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr16:86352701-86352745 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr18:63281666-63281738 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr19:29926234-29926298 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr1:230769615-230769683 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr21:19181972-19182099 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr21:43636204-43636269 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr22:37140286-37140337 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr2:1489652-1489684 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr2:218014858-218014950 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr2:68011946-68011994 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr3:45540738-45540802 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr4:154587735-154587823 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr5:150076323-150076375 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr6:88277128-88277269 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr6:91740224-91740272 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ ├── chr7:84160225-84160277 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi │ └── chr8:124894864-124894916 │ │ ├── base.vcf.gz │ │ ├── base.vcf.gz.tbi │ │ ├── haps.fa │ │ ├── msa.fa │ │ ├── msa.fa.fai │ │ ├── output.vcf.gz │ │ └── output.vcf.gz.tbi ├── cov_results.txt ├── cov_results_xy.txt ├── get_coverage.py ├── get_coverage_counts.py ├── hg38_codis.bed ├── male_cov_results_xy.txt ├── males.txt ├── tmp.vcf.gz.tbi ├── var_counts.txt └── var_counts_sex.txt ├── intersection ├── .gitignore ├── genes │ ├── .gitignore │ ├── README.md │ ├── filt.py │ ├── make_promoters.py │ └── perm_analysis.R └── scripts │ ├── tr_enrichment_counter.py │ └── var_counter.py ├── manuscript ├── .gitignore ├── README.md ├── assembly_numbers │ ├── Analysis.ipynb │ ├── assembly_stats.txt │ ├── coverage_stats.txt │ ├── final_stats.txt │ └── scripts │ │ ├── GRCh38.chrX.PAR.bed │ │ ├── GRCh38_1kg_mainchrs.genome_bedtools.bed │ │ ├── asm_collector.py │ │ ├── calc_n50.py │ │ ├── cov_collector.py │ │ └── sexbed.sh ├── bench_varcnt │ ├── Figure3B.pdf │ ├── Figure3_tier1.pdf │ ├── Figure3_tier1.svg │ ├── Figure3_tier2.pdf │ ├── Figure3_tier2.svg │ ├── Figure3full.pdf │ ├── Figure3full.svg │ ├── README.md │ ├── VariantBenchNumbers.ipynb │ ├── align_replicate.json │ ├── benmark.json │ ├── convert.py │ ├── count_variants.py │ ├── count_variants_bysize.py │ └── rtgdfmaker.py ├── creating_numbers │ ├── Figure2C.pdf │ ├── Figure2D.pdf │ ├── GRCh38_mrg_full_gene.bed │ ├── PathoCodisGeneCoverage.ipynb │ ├── haplotype_similarity.py │ ├── haplotype_similarity.txt.gz │ ├── motif_delta_lengths.ipynb │ ├── new_allele_delta.py │ ├── previous_giab │ │ ├── README.md │ │ ├── make_intersection.sh │ │ ├── report.txt │ │ ├── smallvar_size.txt.gz │ │ └── tr_size.txt.gz │ └── summarize_haplotype_similarity.py ├── diving │ ├── Figure4.pdf │ ├── Figure4.svg │ ├── PopLociDistribution.ipynb │ ├── README.md │ ├── codis.pdf │ ├── codis_PentaE.pdf │ ├── drawing-1.svg │ ├── extract_haps.py │ ├── find_stuff.py │ ├── patho.pdf │ ├── patho_ACAN.pdf │ ├── patho_JPH3.pdf │ ├── patho_TCF4.pdf │ ├── viz.py │ └── vntr.pdf ├── f1_som │ ├── Figure1B.png │ ├── Figure1B_RpN.png │ ├── Figure1MainSOM.png │ ├── Figure1MainSOM_pheno.pdf │ ├── Figure1MainSOM_pheno.png │ ├── Figure2BG.png │ ├── Genes.pdf │ ├── Homopolymer.pdf │ ├── KmerSOM_Adotto.ipynb │ ├── MainSom.pdf │ ├── Microsatellite.pdf │ ├── Promoters.pdf │ ├── RegionPerNeuron.pdf │ ├── SegDups.pdf │ ├── Sup_regperneu_heat.png │ ├── Sup_regperneu_hist.png │ ├── drawing.svg │ └── drawing_b.svg ├── f2_benchmark │ ├── BenchmarkSOM.ipynb │ ├── Figure2B.pdf │ ├── README.md │ ├── SuppTableReplTiers.txt │ ├── hold_motif_delta_lengths.ipynb │ └── sup_NeuronHomPolyDefic.pdf ├── full_figures │ ├── Figure-1.pdf │ ├── Figure-1.png │ ├── Figure-1.svg │ ├── Figure-2.pdf │ ├── Figure-2.png │ ├── Figure3.pdf │ ├── Figure3.png │ ├── Figure4.pdf │ └── Figure4.png ├── result_pathomotifcompare │ ├── MotifMatching.ipynb │ ├── README.md │ └── result.py ├── review_benchmarks │ ├── Analysis.ipynb │ ├── README.md │ ├── ReadLengthAnalysis.ipynb │ ├── round_entropy.py │ └── summary_collector.py ├── reviewer_response_scripts │ ├── buff_query.py │ ├── gc.py │ └── half_query.py ├── sf_trgeneprom │ ├── README.md │ ├── TRGeneProm.pdf │ ├── TRGeneProm_circle.pdf │ ├── TRGeneProm_novl.pdf │ ├── intron_perchromcircle1000.json │ ├── mk_plot.py │ ├── mk_results.sh │ ├── results │ │ ├── CDS_perchromcircle1000.json │ │ ├── CDS_perchromnovl1000.json │ │ ├── UTR_perchromcircle1000.json │ │ ├── UTR_perchromnovl1000.json │ │ ├── intron_perchromcircle1000.json │ │ ├── intron_perchromnovl1000.json │ │ ├── nonintron_perchromcircle1000.json │ │ ├── nonintron_perchromnovl1000.json │ │ ├── promoters_perchromcircle1000.json │ │ ├── promoters_perchromnovl1000.json │ │ ├── transcript_perchromcircle1000.json │ │ └── transcript_perchromnovl1000.json │ └── track_getter.sh ├── sf_upsetplot │ ├── README.md │ ├── make_membership.sh │ ├── make_upset_data.py │ ├── make_upset_plot.py │ └── upsetplot.pdf ├── synthetic_trs │ ├── README.md │ ├── SeqSimulated.pdf │ ├── SeqSimulation.ipynb │ ├── SplitSimulation.ipynb │ ├── similarity_simulation.py │ └── split_simulation.py └── variant_numbers │ ├── Analysis.ipynb │ ├── README.md │ ├── TR_with_any_variant.regioner.json │ ├── TR_without_any_variant.regioner.json │ ├── genome_pVCFcounts.txt │ ├── scripts │ ├── dbsnp_varcounter.py │ ├── pVCF_genome_varcounter.py │ ├── pVCF_varcounter.py │ ├── per_sample_var_numbers.py │ └── run_dbsnp.sh │ └── variants_into_trs.json ├── metadata ├── coverage_files.txt ├── hap_pairs.txt ├── individual_metadata.txt ├── replicate_pairs.txt ├── sample_metadata.txt ├── sample_order.txt └── trio_ids.txt ├── pathogenic ├── .gitignore ├── MukamelRfmt.ipynb ├── Patho.tsv ├── README.md ├── STRipy_scrape.ipynb ├── mukamel.txt ├── patho_autosome.txt ├── patho_cov.txt └── pathogenic_repeats.hg38.bed ├── realignment ├── .gitignore ├── Analysis.ipynb ├── README.md ├── identifying │ └── IdentifyingHeuristics.ipynb ├── scripts │ ├── annotate_tr.sh │ ├── bench_align.sh │ ├── fa_rename.py │ ├── find_blocks.py │ ├── flat.py │ ├── get_reference.py │ ├── mend_fams.txt │ ├── mend_report.sh │ ├── msa2vcf.py │ ├── msa_realign_pipe.sh │ ├── phab_report.py │ ├── remove_redundant.py │ └── vars_per_samp.py └── tiers │ ├── InitialTierAnalysis.ipynb │ ├── README.md │ ├── control_grep.py │ └── pipeline.sh ├── regions ├── .gitignore ├── DataDescription.md ├── HPRC_HG002_Coverage_Analysis.ipynb ├── README.md ├── adotto_hprc │ ├── Notes.txt │ └── make_hq_bed.sh ├── data │ ├── .gitignore │ ├── abundant_pCGG │ │ ├── .gitignore │ │ ├── README.md │ │ └── mk_merge.sh │ ├── baylor │ │ ├── input_spans.txt │ │ ├── merging_stats.json │ │ └── mk_merge.sh │ ├── giab │ │ ├── input_spans.txt │ │ ├── merging_stats.json │ │ └── mk_merge.sh │ ├── input_spans.txt │ ├── input_spans_final.txt │ ├── input_spans_merged.txt │ ├── input_spans_slop.txt │ ├── merging_stats.json │ ├── merging_stats_slop.json │ ├── mk_merge_grand.sh │ ├── pacbio │ │ ├── input_spans.txt │ │ ├── merging_stats.json │ │ └── mk_merge.sh │ ├── region_stats.txt │ ├── ucsd1 │ │ ├── input_spans.txt │ │ ├── merging_stats.json │ │ └── mk_merge.sh │ └── ucsd2 │ │ ├── input_spans.txt │ │ ├── merging_stats.json │ │ └── mk_merge.sh ├── intersection │ ├── .gitignore │ ├── README.md │ ├── Untitled.ipynb │ ├── non_overlapping_annos_per_region.py │ └── variant_region_intersection.py ├── manual_inspection │ ├── giab_input.md │ ├── pacbio_input.md │ └── ucsd1_input.md ├── notebooks │ ├── Cleaning.ipynb │ ├── FinalRegionsQC.ipynb │ ├── NewColumnsSummary.ipynb │ ├── RegionSummary.ipynb │ ├── StrawmanWork.ipynb │ ├── TRQC.ipynb │ ├── analysis.ipynb │ └── intersection.ipynb └── scripts │ ├── add_gene.py │ ├── annotation_improver.py │ ├── append_gene.py │ ├── bed_intersection_stats.py │ ├── bed_stats.py │ ├── boundary_check.py │ ├── calc_inter_stats.py │ ├── consolidate_stats.py │ ├── fasta_splitter.py │ ├── intersection_counter.sh │ ├── make_gene_lookup.py │ ├── merged_bed_filter.py │ ├── remove_gaps.sh │ ├── repeatmasker_on_regions.sh │ ├── repmask_to_joblib.py │ ├── tr_reganno_maker.py │ ├── trf_reformatter.py │ └── update_pathopheno.py ├── slides ├── GIABTRMeeting_ACEnglish_uptoJul212022.pdf ├── GIABTR_Dolzhenko_February212023.pdf ├── GIABTR_English_April182023.pdf ├── GIABTR_English_August92022.pdf ├── GIABTR_English_December132022.pdf ├── GIABTR_English_February72023.pdf ├── GIABTR_English_January102023.pdf ├── GIABTR_English_January242023.pdf ├── GIABTR_English_July252023.pdf ├── GIABTR_English_July262022.pdf ├── GIABTR_English_June272023.pdf ├── GIABTR_English_November12022.pdf ├── GIABTR_English_November152022.pdf ├── GIABTR_English_November292022.pdf ├── GIABTR_English_October172022.pdf ├── GIABTR_English_September202022.pdf ├── GIABTR_English_September42023.pdf ├── GIABTR_English_September62022.pdf ├── GIABTR_Yuan_March212023.pdf ├── GIABTR_Ziaei_March212023.pdf ├── GIABTR_Ziaei_March72023.pdf ├── GIABTR_Zook_January242023.pdf ├── GIABTR_Zook_March212023.pdf ├── GIAB_Tandem_Repeat_Benchmark_Q12023.pdf └── README.md └── variants ├── .gitignore ├── DataDescription.md ├── README.md ├── benchmarking ├── .gitignore ├── Notes.txt ├── README.md ├── inputs │ └── grabber.sh └── scripts │ ├── cmrg_region_bench.sh │ ├── cmrgsv_bench.sh │ ├── experiment1.sh │ ├── experiment3.sh │ ├── full_bench.sh │ ├── mkdf4rtg.py │ ├── phab_bench.py │ ├── phab_gtcounter.py │ └── run_bench.sh ├── data ├── .gitignore ├── hap_mapstats.jl └── misc │ ├── h1_chrY_1xcov.bed │ └── ygap.bed ├── diversity ├── .gitignore ├── README.md ├── UtmosAnalysis.ipynb ├── UtmosPlot.png ├── mk_convert_cmds.sh ├── select_big.txt └── select_small.txt ├── notebooks ├── .gitignore ├── HapotypeCoverage.ipynb ├── SizePerformance.ipynb ├── VariantStats.ipynb └── chrYExplore.ipynb └── scripts ├── agc_map_haplo.sh ├── annotate_cov.py ├── annotate_pvcf_cov.py ├── generate_coverage_tree.py ├── hap_mapstats.py ├── make_anno_jobs.sh ├── map_haplo.sh ├── merge_haps.sh ├── mk_agc_align.sh ├── mk_initial_alignment_jobs.sh ├── mk_mergehaps.sh ├── mk_sq_jobs.sh ├── realignment.sh ├── resolve_gt.py ├── single_sample_cov.py └── 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