├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── chunk ├── .project ├── makefile └── src │ ├── chunk.cpp │ ├── chunker │ ├── chunker_algorithm.cpp │ ├── chunker_header.h │ ├── chunker_io.cpp │ ├── chunker_management.cpp │ ├── chunker_map.cpp │ └── chunker_parameters.cpp │ ├── io │ ├── gmap_reader.cpp │ └── gmap_reader.h │ └── utils │ ├── basic_algos.h │ ├── basic_stats.h │ ├── checksum_utils.h │ ├── compressed_io.h │ ├── otools.h │ ├── random_number.h │ ├── string_utils.h │ ├── timer.h │ └── verbose.h ├── common └── src │ ├── containers │ ├── bitmatrix.cpp │ ├── bitmatrix.h │ ├── ref_haplotype_set.cpp │ ├── ref_haplotype_set.h │ ├── variant_map.cpp │ └── variant_map.h │ ├── io │ ├── gmap_reader.cpp │ ├── gmap_reader.h │ ├── ref_genotype_reader.cpp │ └── ref_genotype_reader.h │ ├── objects │ ├── genotype.cpp │ ├── genotype.h │ ├── variant.cpp │ └── variant.h │ └── utils │ ├── basic_algos.h │ ├── basic_stats.h │ ├── checksum_utils.h │ ├── compressed_io.h │ ├── otools.h │ ├── random_number.h │ ├── string_utils.h │ ├── timer.h │ └── verbose.h ├── concordance ├── makefile └── src │ ├── checker │ ├── checker_finalise.cpp │ ├── checker_header.h │ ├── checker_initialise.cpp │ ├── checker_management.cpp │ └── checker_parameters.cpp │ ├── concordance.cpp │ ├── containers │ ├── call_set_header.h │ ├── call_set_management.cpp │ ├── call_set_reading.cpp │ └── call_set_writing.cpp │ └── utils │ ├── basic_algos.h │ ├── basic_stats.h │ ├── checksum_utils.h │ ├── compressed_io.h │ ├── otools.h │ ├── random_number.h │ ├── string_utils.h │ ├── timer.h │ └── verbose.h ├── docs ├── 404.html ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── Dockerfile ├── Gemfile ├── Gemfile.lock ├── LICENSE.txt ├── README.md ├── Rakefile ├── _config.yml ├── _glossary │ ├── glimpse.md │ ├── imputation.md │ ├── impute.md │ ├── low_coverage.md │ ├── phasing.md │ ├── rap.md │ ├── reference_panel.md │ ├── scaffold.md │ ├── shapeit.md │ ├── singleton.md │ ├── snp_array.md │ ├── switch_error_rate.md │ ├── wes.md │ └── wgs.md ├── _includes │ ├── css │ │ ├── callouts.scss.liquid │ │ ├── custom.scss.liquid │ │ └── just-the-docs.scss.liquid │ ├── favicon.html │ ├── fix_linenos.html │ ├── footer_custom.html │ ├── head.html │ ├── head_custom.html │ ├── header_custom.html │ ├── icons │ │ └── external_link.html │ ├── js │ │ └── custom.js │ ├── mermaid_config.js │ ├── nav.html │ ├── nav_footer_custom.html │ ├── search_placeholder_custom.html │ ├── title.html │ └── vendor │ │ └── anchor_headings.html ├── _layouts │ ├── about.html │ ├── default.html │ ├── home.html │ ├── page.html │ ├── post.html │ ├── table_wrappers.html │ └── vendor │ │ └── compress.html ├── _sass │ ├── base.scss │ ├── buttons.scss │ ├── code.scss │ ├── color_schemes │ │ ├── dark.scss │ │ ├── glimpse2.scss │ │ └── light.scss │ ├── content.scss │ ├── custom │ │ └── custom.scss │ ├── labels.scss │ ├── layout.scss │ ├── modules.scss │ ├── navigation.scss │ ├── print.scss │ ├── search.scss │ ├── skiptomain.scss │ ├── support │ │ ├── _functions.scss │ │ ├── _variables.scss │ │ ├── mixins │ │ │ ├── _buttons.scss │ │ │ ├── _layout.scss │ │ │ ├── _typography.scss │ │ │ └── mixins.scss │ │ └── support.scss │ ├── tables.scss │ ├── typography.scss │ ├── utilities │ │ ├── _colors.scss │ │ ├── _layout.scss │ │ ├── _lists.scss │ │ ├── _spacing.scss │ │ ├── _typography.scss │ │ └── utilities.scss │ └── vendor │ │ ├── OneDarkJekyll │ │ ├── LICENSE │ │ ├── README.md │ │ ├── colors.less │ │ ├── syntax-firewatch-green.scss │ │ ├── syntax-firewatch.scss │ │ ├── syntax-one-dark-vivid.scss │ │ ├── syntax-one-dark.scss │ │ ├── syntax-variables.less │ │ └── syntax.less │ │ └── normalize.scss │ │ ├── README.md │ │ └── normalize.scss ├── assets │ ├── css │ │ ├── just-the-docs-dark.scss │ │ ├── just-the-docs-default.scss │ │ └── just-the-docs-light.scss │ ├── images │ │ ├── accplot.png │ │ ├── branding │ │ │ ├── glimpse_logo.pdf │ │ │ ├── glimpse_logo.svg │ │ │ ├── glimpse_logo_150x64.png │ │ │ ├── glimpse_logo_250x107.png │ │ │ ├── glimpse_logo_300dpi.png │ │ │ └── glimpse_logo_400x171.png │ │ ├── lausanne_icon.jpg │ │ ├── lausanne_logo.jpg │ │ ├── search.svg │ │ ├── sib_logo.jpg │ │ └── snf.gif │ └── js │ │ ├── just-the-docs.js │ │ ├── vendor │ │ └── lunr.min.js │ │ └── zzzz-search-data.json ├── build_localhost.sh ├── docker-compose.yml ├── docs │ ├── documentation │ │ ├── chunk.md │ │ ├── concordance.md │ │ ├── documentation.md │ │ ├── ligate.md │ │ ├── phase.md │ │ └── split_reference.md │ ├── glossary.md │ ├── installation │ │ ├── build_from_source.md │ │ ├── compile_glimpse2.md │ │ ├── docker.md │ │ ├── installation.md │ │ ├── required_libraries.md │ │ ├── static_binaries.md │ │ └── system_requirements.md │ ├── other │ │ └── UKB_Rate_Card-Current_June2021.pdf │ ├── quickstart.md │ └── tutorials │ │ ├── getting_started.md │ │ ├── tutorials.md │ │ ├── ukb_phasing.md │ │ └── ukb_wgs.md ├── favicon.ico ├── glimpse1 │ ├── _config.yml │ ├── commands.html │ ├── css │ │ ├── bootstrap-theme.min.css │ │ ├── bootstrap.min.css │ │ ├── ie10-viewport-bug-workaround.css │ │ └── theme.css │ ├── data │ │ └── rsquare │ │ │ ├── ASW.beagle5.Axiom_UKB_WCSG.na34.annot-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.Axiom_UKB_WCSG.na34.annot-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.GSA-24v2-0_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.GSA-24v2-0_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.GenomeWideSNP_5.na32.annot-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.GenomeWideSNP_5.na32.annot-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.GenomeWideSNP_6.na33.annot-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.GenomeWideSNP_6.na33.annot-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.Human1-2M-DuoCustom_v1_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.Human1-2M-DuoCustom_v1_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.Human670-QuadCustom_v1_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.Human670-QuadCustom_v1_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanCNV370-Quadv3_C-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanCNV370-Quadv3_C-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanCore-12-v1-0-B-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanCore-12-v1-0-B-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanCoreExome-12-v1-1-C-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanCoreExome-12-v1-1-C-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanCoreExome-24v1-0_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanCoreExome-24v1-0_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanExome-12v1-2_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanExome-12v1-2_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanHap300v2_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanHap300v2_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanHap550v3_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanHap550v3_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanHap650Yv3_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanHap650Yv3_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanOmni1S-8v1_H-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanOmni1S-8v1_H-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanOmniExpress-12v1_J-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanOmniExpress-12v1_J-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.HumanOmniExpressExome-8-v1-2-B-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.HumanOmniExpressExome-8-v1-2-B-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumCoreExome-24v1-3_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumCoreExome-24v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumImmunoArray-24v2-0_A-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumImmunoArray-24v2-0_A-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumOmni2-5-8v1-3_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumOmni2-5-8v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumOmni2-5-8v1-4_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumOmni2-5-8v1-4_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumOmni2-5Exome-8v1-3_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumOmni2-5Exome-8v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumOmni5-4v1-2_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumOmni5-4v1-2_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumOmni5Exome-4v1-3_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumOmni5Exome-4v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumOmniExpress-24v1-2_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumOmniExpress-24v1-2_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumOmniExpressExome-8v1-6_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumOmniExpressExome-8v1-6_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.InfiniumPsychArray-24v1-3_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.InfiniumPsychArray-24v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.Multi-EthnicGlobal_A1-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.Multi-EthnicGlobal_A1-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.OmniExpressExome-8v1-1_B-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.OmniExpressExome-8v1-1_B-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.OncoArray-500K-C-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.OncoArray-500K-C-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.PsychArray-B-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.PsychArray-B-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.human610-quadv1_h-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.human610-quadv1_h-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.human660w-quad_v1_h-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.human660w-quad_v1_h-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.humancytosnp-12v2-1_l-b38.source.rsquare.grp.json │ │ │ ├── ASW.beagle5.humancytosnp-12v2-1_l-b38.source.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.humanomni1-quad_v1-0-multi_h-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.humanomni1-quad_v1-0-multi_h-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.beagle5.immuno_beadchip_11419691_b-b38.rsquare.grp.json │ │ │ ├── ASW.beagle5.immuno_beadchip_11419691_b-b38.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov0.1.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov0.1.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov0.2.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov0.2.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov0.3.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov0.3.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov0.4.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov0.4.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov0.5.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov0.5.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov0.6.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov0.6.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov0.8.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov0.8.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov1.0.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov1.0.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov2.0.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov2.0.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov3.0.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov3.0.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov4.0.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov4.0.rsquare.grp.txt.gz │ │ │ ├── ASW.impute.default.cov8.0.rsquare.grp.json │ │ │ ├── ASW.impute.default.cov8.0.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov0.1.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov0.1.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov0.2.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov0.2.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov0.3.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov0.3.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov0.4.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov0.4.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov0.5.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov0.5.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov0.6.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov0.6.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov0.8.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov0.8.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov1.0.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov1.0.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov2.0.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov2.0.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov3.0.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov3.0.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov4.0.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov4.0.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.cov8.0.rsquare.grp.json │ │ │ ├── ASW.phase.default.cov8.0.rsquare.grp.txt.gz │ │ │ ├── ASW.phase.default.covFull.rsquare.grp.json │ │ │ ├── ASW.phase.default.covFull.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.Axiom_UKB_WCSG.na34.annot-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.Axiom_UKB_WCSG.na34.annot-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.GSA-24v2-0_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.GSA-24v2-0_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.GenomeWideSNP_5.na32.annot-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.GenomeWideSNP_5.na32.annot-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.GenomeWideSNP_6.na33.annot-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.GenomeWideSNP_6.na33.annot-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.Human1-2M-DuoCustom_v1_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.Human1-2M-DuoCustom_v1_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.Human670-QuadCustom_v1_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.Human670-QuadCustom_v1_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanCNV370-Quadv3_C-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanCNV370-Quadv3_C-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanCore-12-v1-0-B-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanCore-12-v1-0-B-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanCoreExome-12-v1-1-C-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanCoreExome-12-v1-1-C-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanCoreExome-24v1-0_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanCoreExome-24v1-0_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanExome-12v1-2_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanExome-12v1-2_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanHap300v2_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanHap300v2_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanHap550v3_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanHap550v3_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanHap650Yv3_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanHap650Yv3_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanOmni1S-8v1_H-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanOmni1S-8v1_H-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanOmniExpress-12v1_J-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanOmniExpress-12v1_J-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.HumanOmniExpressExome-8-v1-2-B-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.HumanOmniExpressExome-8-v1-2-B-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumCoreExome-24v1-3_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumCoreExome-24v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumImmunoArray-24v2-0_A-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumImmunoArray-24v2-0_A-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumOmni2-5-8v1-3_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumOmni2-5-8v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumOmni2-5-8v1-4_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumOmni2-5-8v1-4_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumOmni2-5Exome-8v1-3_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumOmni2-5Exome-8v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumOmni5-4v1-2_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumOmni5-4v1-2_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumOmni5Exome-4v1-3_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumOmni5Exome-4v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumOmniExpress-24v1-2_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumOmniExpress-24v1-2_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumOmniExpressExome-8v1-6_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumOmniExpressExome-8v1-6_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.InfiniumPsychArray-24v1-3_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.InfiniumPsychArray-24v1-3_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.Multi-EthnicGlobal_A1-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.Multi-EthnicGlobal_A1-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.OmniExpressExome-8v1-1_B-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.OmniExpressExome-8v1-1_B-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.OncoArray-500K-C-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.OncoArray-500K-C-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.PsychArray-B-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.PsychArray-B-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.human610-quadv1_h-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.human610-quadv1_h-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.human660w-quad_v1_h-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.human660w-quad_v1_h-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.humancytosnp-12v2-1_l-b38.source.rsquare.grp.json │ │ │ ├── EUR.beagle5.humancytosnp-12v2-1_l-b38.source.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.humanomni1-quad_v1-0-multi_h-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.humanomni1-quad_v1-0-multi_h-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.beagle5.immuno_beadchip_11419691_b-b38.rsquare.grp.json │ │ │ ├── EUR.beagle5.immuno_beadchip_11419691_b-b38.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov0.1.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov0.1.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov0.2.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov0.2.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov0.3.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov0.3.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov0.4.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov0.4.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov0.5.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov0.5.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov0.6.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov0.6.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov0.8.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov0.8.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov1.0.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov1.0.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov2.0.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov2.0.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov3.0.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov3.0.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov4.0.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov4.0.rsquare.grp.txt.gz │ │ │ ├── EUR.impute.default.cov8.0.rsquare.grp.json │ │ │ ├── EUR.impute.default.cov8.0.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov0.1.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov0.1.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov0.2.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov0.2.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov0.3.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov0.3.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov0.4.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov0.4.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov0.5.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov0.5.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov0.6.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov0.6.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov0.8.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov0.8.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov1.0.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov1.0.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov2.0.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov2.0.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov3.0.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov3.0.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov4.0.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov4.0.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.cov8.0.rsquare.grp.json │ │ │ ├── EUR.phase.default.cov8.0.rsquare.grp.txt.gz │ │ │ ├── EUR.phase.default.covFull.rsquare.grp.json │ │ │ ├── EUR.phase.default.covFull.rsquare.grp.txt.gz │ │ │ └── txt2json.sh │ ├── fonts │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ ├── images │ │ ├── branding │ │ │ ├── glimpse_icon.png │ │ │ ├── glimpse_logo.pdf │ │ │ ├── glimpse_logo.svg │ │ │ ├── glimpse_logo_150x64.png │ │ │ ├── glimpse_logo_250x107.png │ │ │ ├── glimpse_logo_300dpi.png │ │ │ └── glimpse_logo_400x171.png │ │ ├── lausanne_icon.jpg │ │ ├── lausanne_logo.jpg │ │ ├── overview │ │ │ ├── EMGM_GLIMPSE_website-0.png │ │ │ ├── EMGM_GLIMPSE_website-1.png │ │ │ ├── EMGM_GLIMPSE_website-10.png │ │ │ ├── EMGM_GLIMPSE_website-11.png │ │ │ ├── EMGM_GLIMPSE_website-12.png │ │ │ ├── EMGM_GLIMPSE_website-2.png │ │ │ ├── EMGM_GLIMPSE_website-3.png │ │ │ ├── EMGM_GLIMPSE_website-4.png │ │ │ ├── EMGM_GLIMPSE_website-5.png │ │ │ ├── EMGM_GLIMPSE_website-6.png │ │ │ ├── EMGM_GLIMPSE_website-7.png │ │ │ ├── EMGM_GLIMPSE_website-8.png │ │ │ └── EMGM_GLIMPSE_website-9.png │ │ ├── sib_logo.jpg │ │ ├── snf.gif │ │ └── tutorials │ │ │ ├── accplot.png │ │ │ ├── accplot_hg19.png │ │ │ └── chrX.png │ ├── index.html │ ├── installation.html │ ├── navbar.html │ ├── overview.html │ ├── rsquare_asw.html │ ├── rsquare_eur.html │ ├── script │ │ ├── Chart.min.js │ │ ├── bootstrap.min.js │ │ ├── docs.min.js │ │ ├── ie10-viewport-bug-workaround.js │ │ └── jquery-1.12.4.min.js │ ├── tutorial_b38.html │ ├── tutorial_chrX.html │ └── tutorial_hg19.html ├── index.md ├── just-the-docs.gemspec ├── lib │ └── tasks │ │ └── search.rake ├── package-lock.json └── package.json ├── ligate ├── makefile └── src │ ├── ligate.cpp │ ├── ligater │ ├── ligater_algorithm.cpp │ ├── ligater_finalise.cpp │ ├── ligater_header.h │ ├── ligater_initialise.cpp │ ├── ligater_management.cpp │ └── ligater_parameters.cpp │ └── utils │ ├── basic_algos.h │ ├── basic_stats.h │ ├── checksum_utils.h │ ├── compressed_io.h │ ├── otools.h │ ├── random_number.h │ ├── string_utils.h │ ├── timer.h │ └── verbose.h ├── makefile ├── maps ├── genetic_maps.b37 │ ├── chr1.b37.gmap.gz │ ├── chr10.b37.gmap.gz │ ├── chr11.b37.gmap.gz │ ├── chr12.b37.gmap.gz │ ├── chr13.b37.gmap.gz │ ├── chr14.b37.gmap.gz │ ├── chr15.b37.gmap.gz │ ├── chr16.b37.gmap.gz │ ├── chr17.b37.gmap.gz │ ├── chr18.b37.gmap.gz │ ├── chr19.b37.gmap.gz │ ├── chr2.b37.gmap.gz │ ├── chr20.b37.gmap.gz │ ├── chr21.b37.gmap.gz │ ├── chr22.b37.gmap.gz │ ├── chr3.b37.gmap.gz │ ├── chr4.b37.gmap.gz │ ├── chr5.b37.gmap.gz │ ├── chr6.b37.gmap.gz │ ├── chr7.b37.gmap.gz │ ├── chr8.b37.gmap.gz │ ├── chr9.b37.gmap.gz │ ├── chrX.b37.gmap.gz │ ├── chrX_par1.b37.gmap.gz │ └── chrX_par2.b37.gmap.gz └── genetic_maps.b38 │ ├── chr1.b38.gmap.gz │ ├── chr10.b38.gmap.gz │ ├── chr11.b38.gmap.gz │ ├── chr12.b38.gmap.gz │ ├── chr13.b38.gmap.gz │ ├── chr14.b38.gmap.gz │ ├── chr15.b38.gmap.gz │ ├── chr16.b38.gmap.gz │ ├── chr17.b38.gmap.gz │ ├── chr18.b38.gmap.gz │ ├── chr19.b38.gmap.gz │ ├── chr2.b38.gmap.gz │ ├── chr20.b38.gmap.gz │ ├── chr21.b38.gmap.gz │ ├── chr22.b38.gmap.gz │ ├── chr3.b38.gmap.gz │ ├── chr4.b38.gmap.gz │ ├── chr5.b38.gmap.gz │ ├── chr6.b38.gmap.gz │ ├── chr7.b38.gmap.gz │ ├── chr8.b38.gmap.gz │ ├── chr9.b38.gmap.gz │ ├── chrX.b38.gmap.gz │ ├── chrX_par1.b38.gmap.gz │ └── chrX_par2.b38.gmap.gz ├── phase ├── .project ├── makefile └── src │ ├── caller │ ├── caller_algorithm.cpp │ ├── caller_finalise.cpp │ ├── caller_header.h │ ├── caller_initialise.cpp │ ├── caller_management.cpp │ └── caller_parameters.cpp │ ├── containers │ ├── bitmatrix.cpp │ ├── bitmatrix.h │ ├── conditioning_set.cpp │ ├── conditioning_set.h │ ├── genotype_set.cpp │ ├── genotype_set.h │ ├── glimpse_mpileup.cpp │ ├── glimpse_mpileup.h │ ├── haplotype_set.cpp │ ├── haplotype_set.h │ ├── ref_haplotype_set.cpp │ ├── ref_haplotype_set.h │ ├── variant_map.cpp │ └── variant_map.h │ ├── io │ ├── genotype_bam_caller.cpp │ ├── genotype_bam_caller.h │ ├── genotype_reader.cpp │ ├── genotype_reader.h │ ├── genotype_writer.cpp │ ├── genotype_writer.h │ ├── gmap_reader.cpp │ └── gmap_reader.h │ ├── main.cpp │ ├── models │ ├── imputation_hmm.cpp │ ├── imputation_hmm.h │ ├── phasing_hmm.cpp │ └── phasing_hmm.h │ ├── objects │ ├── genotype.cpp │ ├── genotype.h │ ├── variant.cpp │ └── variant.h │ └── utils │ ├── basic_algos.h │ ├── basic_stats.h │ ├── checksum_utils.h │ ├── compressed_io.h │ ├── otools.h │ ├── random_number.h │ ├── string_utils.h │ ├── timer.h │ └── verbose.h ├── resources └── chunks │ └── b38 │ ├── 4cM │ ├── chunks_chr1.txt │ ├── chunks_chr10.txt │ ├── chunks_chr11.txt │ ├── chunks_chr12.txt │ ├── chunks_chr13.txt │ ├── chunks_chr14.txt │ ├── chunks_chr15.txt │ ├── chunks_chr16.txt │ ├── chunks_chr17.txt │ ├── chunks_chr18.txt │ ├── chunks_chr19.txt │ ├── chunks_chr2.txt │ ├── chunks_chr20.txt │ ├── chunks_chr21.txt │ ├── chunks_chr22.txt │ ├── chunks_chr3.txt │ ├── chunks_chr4.txt │ ├── chunks_chr5.txt │ ├── chunks_chr6.txt │ ├── chunks_chr7.txt │ ├── chunks_chr8.txt │ └── chunks_chr9.txt │ └── README ├── split_reference ├── makefile ├── src │ ├── caller │ │ ├── caller_algorithm.cpp │ │ ├── caller_finalise.cpp │ │ ├── caller_header.h │ │ ├── caller_initialise.cpp │ │ ├── caller_management.cpp │ │ └── caller_parameters.cpp │ ├── containers │ │ ├── bitmatrix.cpp │ │ ├── bitmatrix.h │ │ ├── ref_haplotype_set.cpp │ │ ├── ref_haplotype_set.h │ │ ├── variant_map.cpp │ │ └── variant_map.h │ ├── io │ │ ├── gmap_reader.cpp │ │ ├── gmap_reader.h │ │ ├── ref_genotype_reader.cpp │ │ └── ref_genotype_reader.h │ ├── main.cpp │ ├── objects │ │ ├── genotype.cpp │ │ ├── genotype.h │ │ ├── variant.cpp │ │ └── variant.h │ └── utils │ │ ├── basic_algos.h │ │ ├── basic_stats.h │ │ ├── checksum_utils.h │ │ ├── compressed_io.h │ │ ├── otools.h │ │ ├── random_number.h │ │ ├── string_utils.h │ │ ├── timer.h │ │ └── verbose.h └── xsqueezeit │ ├── Makefile │ ├── accessor.cpp │ ├── bcf_traversal.cpp │ ├── c_api.cpp │ ├── include │ ├── accessor.hpp │ ├── accessor_internals.hpp │ ├── accessor_internals_new.hpp │ ├── bcf_traversal.hpp │ ├── block.hpp │ ├── c_api.h │ ├── compression.hpp │ ├── constexpr.hpp │ ├── fs.hpp │ ├── gt_block.hpp │ ├── interfaces.hpp │ ├── internal_gt_record.hpp │ ├── make_unique.hpp │ ├── wah.hpp │ ├── xcf.hpp │ └── xsi_mixed_vcf.hpp │ ├── xcf.cpp │ └── xsi_mixed_vcf.cpp ├── tutorial ├── GLIMPSE_validation │ ├── EUR.validation.NA12878.chr22.bcf │ ├── EUR.validation.NA12878.chr22.bcf.csi │ ├── gnomad.genomes.r3.0.sites.chr22.isec.bcf │ └── gnomad.genomes.r3.0.sites.chr22.isec.bcf.csi ├── NA12878_1x_bam │ ├── NA12878.bam │ └── NA12878.bam.bai ├── concordance.lst ├── plot │ ├── accplot.png │ └── concordance_plot.py ├── reference_genome │ ├── hs38DH.chr22.fa.gz │ ├── hs38DH.chr22.fa.gz.fai │ └── hs38DH.chr22.fa.gz.gzi ├── step1_script_setup.sh ├── step2_script_reference_panel.sh ├── step3_script_chunk.sh ├── step4_script_split_reference.sh ├── step5_script_impute.sh ├── step6_script_ligate.sh ├── step7_script_concordance.sh └── step8_script_cleanup.sh └── versions └── versions.h /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odelaneau/GLIMPSE/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odelaneau/GLIMPSE/HEAD/Dockerfile 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