├── .gitignore ├── LICENSE.vg.txt ├── README.md ├── aws-speed-notes.txt └── scripts ├── allele_balance_plot ├── README.md ├── kubernetes_pileup_call └── plot_allele_balance.py ├── archiving ├── README.md ├── archive-readme.md ├── archive_code_containers_and_products.sh ├── products-readme.md ├── save_construction_inputs.sh ├── save_mapping_inputs.sh └── software-readme.md ├── construction ├── 01_make_HGSVC_graph.sh ├── 02_move_HGSVC_graph.sh ├── 03_make_primary_graph.sh ├── 04_make_1000GPlons_GRCh38_graph.sh ├── 05_make_1000GPlons_GRCh38_graph_with_gcsa.sh ├── 06_yeast_graphs_and_reads.sh └── README.md ├── genotyping ├── README.md ├── graphtyper_kubernetes ├── real_read_deepvariant_call.sh └── real_read_dragen_call.sh ├── indexing ├── 01_make_HGSVC_processed_gbwts.sh ├── 02_make_HGSVC_processed_gbwt_indexes.sh ├── 03_make_HGSVC_alt_xg.sh ├── 04_prune_HGSVC.sh ├── 05_make_HGSVC_gcsa.sh ├── 06_make_1000GPlons_GRCh38_sampled_gbwts.sh ├── 07_make_1000GPlons_GRCh38_cover_gbwts.sh ├── 08_make_positive_control_gbwts.sh ├── 09_make_1000GPlons_full_gbwt.sh ├── 10_make_HGSVC_annotation_xg.sh ├── 11_make_primary_paths_gbwt.sh ├── 12_make_primary_cover_gbwt.sh └── README.md ├── mapping ├── README.md ├── assess_mappability.py ├── combine_reads.py ├── giraffe_accuracy_kubernetes ├── giraffe_accuracy_primary_kubernetes ├── giraffe_control_accuracy_kubernetes ├── giraffe_gbwts_accuracy_kubernetes ├── giraffe_speed.sh ├── giraffe_yeast_experiment.sh ├── graphaligner_accuracy_kubernetes ├── graphaligner_speed.sh ├── hisat2 │ ├── 00_hisat2_prepare_variants_1kg.sh │ ├── 00_hisat2_prepare_variants_hgsvc.sh │ ├── 01_hisat2_generate_index.sh │ ├── 02_hisat2_map_reads_1kg.sh │ ├── 02_hisat2_map_reads_hgsvc.sh │ ├── 03_hisat2_calc_map_stats_1kg.sh │ ├── 03_hisat2_calc_map_stats_hgsvc.sh │ └── README.md ├── hisat2_accuracy_kubernetes ├── hisat2_speed.sh ├── linear_mappers_accuracy_kubernetes ├── linear_mappers_speed.sh ├── map_accuracy_kubernetes ├── map_accuracy_primary_kubernetes ├── map_speed.sh └── real_read_experiments │ ├── README.md │ ├── bwamem_map.sh │ ├── dragen_map.sh │ ├── giraffe_map.sh │ └── vg_map.sh ├── plotting ├── README.md ├── plot-gbwt-rocs.sh ├── plot-qq-comparing-aligners.R ├── plot-qq.R ├── plot-roc-comparing-aligners.R ├── plot-roc.R ├── plot-rocs.sh ├── plot_real_speed.py ├── speed_report_hiseq2500.tsv ├── speed_report_hiseqxten.tsv └── speed_report_novaseq6000.tsv ├── prep ├── 01_make_reference.sh ├── 02_preprocess_1000GPlons_VCFs.sh └── README.md ├── read_simulation ├── README.md ├── simulate-1000gp.sh └── simulate-hgsvc.sh └── sv ├── .gitignore ├── README.md ├── combine-sv-genotypes ├── README.md ├── align_variants.py ├── annotate-sv-loci-2504kgp.R ├── annotate-sv-loci-mesa2k.R └── merge_exact_hets.py ├── describe-svs ├── 1kgp-info.tsv ├── 2504kgp.svsite80al.ac.pcs.rds ├── README.md ├── annotate-svs-functional.Rmd ├── annotate-svs-functional.md ├── annotate-svs-functional_files │ └── figure-gfm │ │ ├── eqtlcontrols-1.png │ │ ├── eqtlenr-1.png │ │ └── popspec-1.png ├── compare-public-catalogs.Rmd ├── compare-public-catalogs.md ├── compare-public-catalogs.tex ├── compare-public-catalogs_files │ └── figure-gfm │ │ ├── fig-1.png │ │ ├── freq_dist-1.png │ │ ├── freq_dist-2.png │ │ ├── freq_dist-3.png │ │ ├── freq_dist-4.png │ │ ├── freq_dist-5.png │ │ ├── freqcomp_gnomad-1.png │ │ ├── freqcomp_gnomad-2.png │ │ ├── freqcomp_gnomad-3.png │ │ ├── freqcomp_gnomad-4.png │ │ ├── freqcomp_kgp3-1.png │ │ ├── freqcomp_kgp3-2.png │ │ ├── freqcomp_kgp3-3.png │ │ ├── freqcomp_kgp3-4.png │ │ ├── freqcomp_svpop-1.png │ │ ├── freqcomp_svpop-2.png │ │ ├── freqcomp_svpop-3.png │ │ ├── freqcomp_svpop-4.png │ │ ├── svpop_vs_gnomad-1.png │ │ ├── svpop_vs_gnomad-2.png │ │ ├── svpop_vs_gnomad-3.png │ │ └── svpop_vs_gnomad-4.png ├── examples-svsites-mesa.Rmd ├── examples-svsites-mesa.md ├── examples-svsites-mesa.pdf ├── examples-svsites-mesa_files │ └── figure-gfm │ │ ├── del-clique-1.png │ │ ├── del-clique-2.png │ │ ├── del-clique-3.png │ │ ├── del-clique-4.png │ │ ├── del-clique-5.png │ │ ├── del-clique-major-1.png │ │ ├── del-clique-major-2.png │ │ ├── del-clique-major-3.png │ │ ├── del-notclique-1.png │ │ ├── del-notclique-2.png │ │ ├── del-notclique-3.png │ │ ├── del-notclique-4.png │ │ ├── del-notclique-5.png │ │ ├── del-notclique-6.png │ │ ├── ex-1.png │ │ ├── ex-2.png │ │ ├── ex-3.png │ │ ├── ex-4.png │ │ ├── ins-clique-1.png │ │ ├── ins-clique-2.png │ │ ├── ins-clique-3.png │ │ ├── ins-clique-4.png │ │ ├── ins-clique-5.png │ │ ├── ins-clique-6.png │ │ ├── ins-clique-major-1.png │ │ ├── ins-clique-major-2.png │ │ ├── ins-clique-major-3.png │ │ ├── ins-notclique-1.png │ │ ├── ins-notclique-2.png │ │ ├── ins-notclique-3.png │ │ ├── ins-notclique-4.png │ │ ├── ins-notclique-5.png │ │ └── ins-notclique-6.png ├── figs │ ├── examples-svsites-mesa-long.pdf │ ├── examples-svsites-mesa.pdf │ ├── fig-pops-freq-kgp.pdf │ ├── fig-pops-freq-mesa.pdf │ ├── fig-sv-1kgp-pcs.pdf │ ├── fig-sv-1kgp-stats.pdf │ ├── fig-sv-freq-comp.pdf │ ├── fig-sv-functional-summary.pdf │ ├── fig-sv-mesa-pcs.pdf │ ├── fig-sv-mesa-stats-2.pdf │ └── fig-sv-mesa-stats.pdf ├── files-README.md ├── fine-tune-eval.Rmd ├── fine-tune-eval.md ├── fine-tune-eval_files │ └── figure-gfm │ │ └── perm-1.png ├── mesa2k.svsite80al.ac.pcs.sdev.tsv ├── pca-1kgp.Rmd ├── pca-1kgp.md ├── pca-1kgp_files │ └── figure-gfm │ │ ├── fig-1.png │ │ ├── svpc-1.png │ │ ├── svpc-2.png │ │ ├── svpc-3.png │ │ ├── svtsne-1.png │ │ └── svtsne-2.png ├── pca-mesa-1kgp.Rmd ├── pca-mesa.Rmd ├── pca-mesa.md ├── pca-mesa_files │ └── figure-gfm │ │ ├── fig-1.png │ │ ├── fig-2.png │ │ ├── fig-3.png │ │ ├── pc-1.png │ │ ├── pc-2.png │ │ ├── pc-3.png │ │ ├── pc-4.png │ │ ├── sv-1.png │ │ ├── sv-2.png │ │ ├── sv-3.png │ │ ├── svtsne-1.png │ │ ├── topmed_cl-1.png │ │ └── topmed_cl-2.png ├── pedigree.tsv ├── pops-freq-1kgp-med1.tsv ├── pops-freq-1kgp.Rmd ├── pops-freq-1kgp.md ├── pops-freq-1kgp_files │ └── figure-gfm │ │ ├── ex_freq-1.png │ │ ├── ex_rare-1.png │ │ ├── fig-1.png │ │ ├── freqmmm-1.png │ │ ├── popspec-1.png │ │ ├── popspec_type_size-1.png │ │ └── popspec_type_size-2.png ├── pops-freq-mesa.Rmd ├── pops-freq-mesa.md ├── pops-freq-mesa_files │ └── figure-gfm │ │ ├── fig-1.png │ │ ├── freqmmm-1.png │ │ ├── pcs-1.png │ │ ├── pcs-2.png │ │ ├── popspec-1.png │ │ ├── popspec_type_size-1.png │ │ └── popspec_type_size-2.png ├── prepare-public-catalogs.R ├── prepare-public-catalogs.Rmd ├── prepare-public-catalogs.md ├── public-sv-catalogs.RData ├── summary-sv-stats-1kgp.Rmd ├── summary-sv-stats-1kgp.md ├── summary-sv-stats-1kgp_files │ └── figure-gfm │ │ ├── af-1.png │ │ ├── af-2.png │ │ ├── fig-1.png │ │ ├── site-al-1.png │ │ ├── site-al-2.png │ │ └── size-1.png ├── summary-sv-stats-mesa.Rmd ├── summary-sv-stats-mesa.md ├── summary-sv-stats-mesa_files │ └── figure-gfm │ │ ├── af-1.png │ │ ├── af-2.png │ │ ├── fig-1.png │ │ ├── fig-2.png │ │ ├── site-al-1.png │ │ ├── site-al-2.png │ │ └── size-1.png └── svsite.2504kgp.novel.tsv ├── eqtl ├── README.md ├── eqtl-summary-snv-indel-sv.Rmd ├── eqtl-summary-snv-indel-sv.md ├── eqtl-summary-snv-indel-sv_files │ └── figure-gfm │ │ ├── effect.size-1.png │ │ ├── ex-1.png │ │ ├── ex-2.png │ │ ├── ex-3.png │ │ ├── ex-4.png │ │ ├── fig-1.png │ │ ├── qc-1.png │ │ ├── qc-2.png │ │ ├── qc-3.png │ │ ├── qc-4.png │ │ ├── qc-5.png │ │ ├── qc-6.png │ │ ├── sv.ge-1.png │ │ └── sv.ge-2.png ├── eqtl-summary.Rmd ├── eqtl-summary.md ├── eqtl-summary.tex ├── eqtl-summary_files │ └── figure-gfm │ │ ├── effect.size-1.png │ │ ├── ex-1.png │ │ ├── ex-2.png │ │ ├── ex-3.png │ │ ├── ex-4.png │ │ ├── fig-1.png │ │ ├── norm-1.png │ │ ├── norm-10.png │ │ ├── norm-11.png │ │ ├── norm-12.png │ │ ├── norm-2.png │ │ ├── norm-3.png │ │ ├── norm-4.png │ │ ├── norm-5.png │ │ ├── norm-6.png │ │ ├── norm-7.png │ │ ├── norm-8.png │ │ ├── norm-9.png │ │ ├── qc-1.png │ │ ├── qc-2.png │ │ ├── qc-3.png │ │ ├── qc-4.png │ │ ├── qc-5.png │ │ └── qc-6.png ├── fig-sv-eqtl.pdf ├── fig-sv-snv-indel-eqtl.pdf ├── files-README.md ├── find-eqtls-all-variants.R ├── find-eqtls.R └── subset-vcf.py ├── genotype-svs ├── README.md ├── fig-sv-trio-eval.pdf ├── fig-sveval-ind.pdf ├── fig-sveval.pdf ├── giab-vg_graphtyper-sveval-prcurve.tsv ├── giab6_hg37-sveval-prcurve.tsv ├── giab6_hg38-sveval-prcurve.tsv ├── graphtyper_kubernetes ├── hgsvc-hsvlr-40x-sveval-prcurve.tsv ├── hgsvc-hsvlr-sveval-prcurve.tsv ├── hgsvc-map-sveval-prcurve.tsv ├── hgsvc-vg_graphtyper-sveval-prcurve.tsv ├── hgsvcsim-vg_graphtyper-sveval-prcurve.tsv ├── inputs.json ├── outputs.json ├── resource-stats.Rmd ├── resource-stats.md ├── resource-stats.tex ├── resource-stats_files │ └── figure-gfm │ │ ├── corehours-1.png │ │ ├── corehours-2.png │ │ ├── corehours_underest-1.png │ │ ├── corehours_underest-2.png │ │ └── nshards_sample-1.png ├── sv-evaluation.Rmd ├── sv-evaluation.md ├── sv-evaluation_files │ └── figure-gfm │ │ ├── depth-1.png │ │ ├── depth-2.png │ │ ├── depth-3.png │ │ ├── fig-1.png │ │ ├── fig-2.png │ │ ├── graphs-1.png │ │ ├── graphs-2.png │ │ ├── graphs-3.png │ │ ├── map-1.png │ │ ├── map-2.png │ │ ├── map-3.png │ │ ├── vg_graphtyper-1.png │ │ ├── vg_graphtyper-2.png │ │ └── vg_graphtyper-3.png ├── sv-trio-evaluation.Rmd ├── sv-trio-evaluation.md ├── sv-trio-evaluation_files │ └── figure-gfm │ │ ├── fig-1.png │ │ ├── me.gq-1.png │ │ ├── sv.gq-1.png │ │ └── tr.gq-1.png ├── terra-1kgp-subs-resources.tsv.gz └── terra-mesa-subs-resources.tsv.gz ├── make-graph-indexes ├── Dockerfile ├── README.md ├── Snakefile └── snakemake_config.yaml ├── make-graph ├── Dockerfile ├── README.md ├── Snakefile ├── chunkedAugmentation.py ├── chunkedConstruction.py ├── makeConcatCmd.py ├── prepareAugmentFiles.py └── prepareVcf.R ├── merge-svs ├── README.md ├── filter.R ├── liftVcf.py └── removeInfo.py ├── remap-to-dedup-merged-svs ├── README.md ├── Snakefile ├── extractCluster.py ├── findDups.R ├── mergeRemapResults.R └── select1kgp.R └── save-data-to-archive.md /.gitignore: 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