LICENSE
MANIFEST.in
NexteraRapidCapture-45807-probes.txt
NexteraRapidCapture-45807-targeted-regions.txt
README.md
api-test.py
gemini-bed-format.py
gemini_install.py
master-test.sh
requirements.txt
runs.roh.txt
setup.cfg
setup.py
test.txt
docs/.DS_Store
docs/EXAMPLES.rst
docs/Makefile
docs/TODO.rst
docs/build.sh
docs/conf.py
docs/gemini.ai
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gemini/GeminiQuery.py
gemini/__init__.py
gemini/anno_info.py
gemini/annotations.py
gemini/compression.py
gemini/config.py
gemini/database.py
gemini/dgidb.py
gemini/func_impact.py
gemini/gemini_actionable_mutations.py
gemini/gemini_amend.py
gemini/gemini_annotate.py
gemini/gemini_browser.py
gemini/gemini_constants.py
gemini/gemini_dbinfo.py
gemini/gemini_dump.py
gemini/gemini_inheritance_model_utils.py
gemini/gemini_load.py
gemini/gemini_load_chunk.py
gemini/gemini_main.py
gemini/gemini_merge_chunks.py
gemini/gemini_plot.py
gemini/gemini_query.py
gemini/gemini_region.py
gemini/gemini_set_somatic.py
gemini/gemini_stats.py
gemini/gemini_subjects.py
gemini/gemini_update.py
gemini/gemini_utils.py
gemini/gemini_windower.py
gemini/gene_table.py
gemini/infotag.py
gemini/install-data.py
gemini/merge-bed.py
gemini/ped.py
gemini/popgen.py
gemini/severe_impact.py
gemini/snpEff.py
gemini/sql.py
gemini/sql_extended.py
gemini/sql_utils.py
gemini/stats.py
gemini/tool_autosomal_dominant.py
gemini/tool_autosomal_recessive.py
gemini/tool_burden_tests.py
gemini/tool_compound_hets.py
gemini/tool_de_novo_mutations.py
gemini/tool_homozygosity_runs.py
gemini/tool_interactions.py
gemini/tool_lof_sieve.py
gemini/tool_mendel_errors.py
gemini/tool_pathways.py
gemini/vcf_info.py
gemini/vep.py
gemini/version.py
gemini.egg-info/PKG-INFO
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gemini.egg-info/not-zip-safe
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gemini.egg-info/top_level.txt
gemini/annotation_provenance/make-1000G.sh
gemini/annotation_provenance/make-29way-conservation.sh
gemini/annotation_provenance/make-cadd.sh
gemini/annotation_provenance/make-cancer-census.sh
gemini/annotation_provenance/make-clinvar.sh
gemini/annotation_provenance/make-cosmic.sh
gemini/annotation_provenance/make-cse.sh
gemini/annotation_provenance/make-dbsnp.sh
gemini/annotation_provenance/make-encode-chrom-segs.sh
gemini/annotation_provenance/make-encode-tfbs-clustering.sh
gemini/annotation_provenance/make-esp-variants.sh
gemini/annotation_provenance/make-gerp.sh
gemini/annotation_provenance/make-ncbi-grc-patches.py
gemini/annotation_provenance/make-pfam-ucsc.sh
gemini/annotation_provenance/make-polyphen2.sh
gemini/annotation_provenance/make-recombination.sh
gemini/annotation_provenance/make-rmsk-meta.sh
gemini/annotation_provenance/make-stam-125-cells-dnase1-clusters.sh
gemini/annotation_provenance/make-vista-enchancers.sh
gemini/annotation_provenance/HPRD/hprd_graph.py
gemini/annotation_provenance/KEGG/KEGG_REST_files/all_kegg_hsa_to_uniprot
gemini/annotation_provenance/KEGG/KEGG_REST_files/kegg_hsa_to_gene
gemini/annotation_provenance/KEGG/KEGG_REST_files/kegg_hsa_to_path
gemini/annotation_provenance/KEGG/KEGG_REST_files/note
gemini/annotation_provenance/KEGG/KEGG_REST_files/pathways
gemini/annotation_provenance/KEGG/make_path_files/add_path
gemini/annotation_provenance/KEGG/make_path_files/ensembl_genes66
gemini/annotation_provenance/KEGG/make_path_files/format.sh
gemini/annotation_provenance/KEGG/make_path_files/kegg_hsa_to_gene_fmt
gemini/annotation_provenance/KEGG/make_path_files/kegg_pathway
gemini/annotation_provenance/KEGG/make_path_files/map_uni2hsa2gene
gemini/annotation_provenance/KEGG/make_path_files/mart_export_transcripts66.txt
gemini/annotation_provenance/KEGG/make_path_files/mart_header
gemini/annotation_provenance/KEGG/make_path_files/unihsagene.py
gemini/annotation_provenance/KEGG/make_path_files/uniprot_hsa_map
gemini/annotation_provenance/gene_table/README
gemini/annotation_provenance/gene_table/combined_gene_table.py
gemini/annotation_provenance/gene_table/ensembl.py
gemini/annotation_provenance/gene_table/map_entrez.py
gemini/annotation_provenance/gene_table/synonym.py
gemini/annotation_provenance/gene_table/anno_files/HMD_HumanPhenotype.rpt
gemini/annotation_provenance/gene_table/anno_files/genic_intolerance_dataset2
gemini/annotation_provenance/gene_table/downloads/HGNC_download
gemini/annotation_provenance/gene_table/downloads/hgnc.query.pl
gemini/annotation_provenance/gene_table/downloads/mart_export1
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gemini/annotation_provenance/gene_table/downloads/mart_export3
gemini/annotation_provenance/gene_table/downloads/query1.pl
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gemini/data/__init__.py
gemini/data/gemini.conf
gemini/scripts/.DS_Store
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gemini/scripts/__init__.pyc
gemini/scripts/gemini
gemini/scripts/gemini_install.py
gemini/static/.DS_Store
gemini/static/tmp.txt
gemini/static/css/.DS_Store
gemini/static/css/gemini.css
gemini/static/img/gemini.png
gemini/static/third_party/.DS_Store
gemini/static/third_party/bootstrap/.DS_Store
gemini/static/third_party/bootstrap/css/.DS_Store
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gemini/views/auto_dom.j2.html
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test/.DS_Store
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test/=13.1.0
test/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.snippet.snpEff.vcf
test/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.snippet.vcf
test/data-setup.sh
test/exp
test/foo.log
test/obs
test/test-amend.sh
test/test-annotate-tool.sh
test/test-auto-dom.sh
test/test-auto-rec.sh
test/test-burden.sh
test/test-cadd.sh
test/test-clinvar.sh
test/test-columns.sh
test/test-comphet.sh
test/test-de-novo.sh
test/test-dump.sh
test/test-effstring.sh
test/test-encode.sh
test/test-genome.sh
test/test-genotypes.sh
test/test-gerp.sh
test/test-interactions.sh
test/test-load.sh
test/test-lofsieve.sh
test/test-map.sh
test/test-pathtool.sh
test/test-pfam.sh
test/test-pop.sh
test/test-query.sh
test/test-region.sh
test/test-roh.sh
test/test-stats.sh
test/test-wildcards.sh
test/test-windower.sh
test/test.aaf.vcf
test/test.auto_dom.no_parents.2.ped
test/test.auto_dom.no_parents.2.vcf
test/test.auto_dom.no_parents.3.ped
test/test.auto_dom.no_parents.3.vcf
test/test.auto_dom.no_parents.4.ped
test/test.auto_dom.no_parents.4.vcf
test/test.auto_dom.no_parents.5.ped
test/test.auto_dom.no_parents.5.vcf
test/test.auto_dom.no_parents.ped
test/test.auto_dom.no_parents.vcf
test/test.auto_dom.ped
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test/test.auto_rec.no_parents.2.ped
test/test.auto_rec.no_parents.2.vcf
test/test.auto_rec.no_parents.3.ped
test/test.auto_rec.no_parents.3.vcf
test/test.auto_rec.no_parents.4.ped
test/test.auto_rec.no_parents.4.vcf
test/test.auto_rec.no_parents.5.ped
test/test.auto_rec.no_parents.5.vcf
test/test.auto_rec.no_parents.ped
test/test.auto_rec.no_parents.vcf
test/test.auto_rec.ped
test/test.auto_rec.vcf
test/test.auto_rec.vcf.vcfidx
test/test.burden.ped
test/test.burden.vcf
test/test.cadd.vcf
test/test.clinvar.vcf
test/test.comp_het.2.vcf
test/test.comp_het.ped
test/test.comp_het.vcf
test/test.de_novo.ped
test/test.de_novo.vcf
test/test.family.vcf
test/test.passonly.vcf
test/test.query.vcf
test/test.region.vep.vcf
test/test.roh.vcf
test/test.snpeff.vcf
test/test.vcf_id.snpeff.vcf
test/test1.snpeff.vcf
test/test2.snpeff.vcf
test/test3.snpeff.vcf
test/test4.snpeff.ped
test/test4.vep.snpeff.vcf
test/test5.vep.snpeff.vcf
test/test_amend_sample.ped
test/test_extended_ped.ped