glow
An open-source toolkit for large-scale genomic analysis
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- org.apache.spark.sql.sources.DataSourceRegister
- org.apache.spark.sql.SparkSessionExtensionsProvider
- functions.yml
- VCFHeaderWriter.scala
- VCFEncoderUtils.scala
- BgenConverterUtils.scala
- BgenFileFormat.scala
- BgenFileIterator.scala
- BgenGenotypeReader.scala
- BgenHeaderWriter.scala
- BgenRecordWriter.scala
- BgenRowToInternalRowConverter.scala
- BgenSchemaInferrer.scala
- BigBgenDatasource.scala
- InternalRowToBgenRowConverter.scala
- HlsEventRecorder.scala
- HlsUsageLogging.scala
- ConverterUtils.scala
- datasourceOptions.scala
- GlowLogging.scala
- HailUtils.scala
- HasStringency.scala
- Named.scala
- PythonUtils.scala
- schemas.scala
- SimpleInterval.scala
- WithUtils.scala
- GffDataSource.scala
- BedFileIterator.scala
- PlinkFileFormat.scala
- PlinkRowToInternalRowConverter.scala
- package.scala
- CovariateQRContext.scala
- ExpressionHelper.scala
- FirthTest.scala
- glueExpressions.scala
- LiftOverCoordinatesExpr.scala
- LikelihoodRatioTest.scala
- LinearRegressionExpr.scala
- LinearRegressionGwas.scala
- LogisticRegressionExpr.scala
- LogisticRegressionGwas.scala
- MeanSubstitute.scala
- MomentAggState.scala
- NormalizeVariantExpr.scala
- PerSampleSummaryStatistics.scala
- SampleCallSummaryStats.scala
- VariantQcExprs.scala
- VariantUtilExprs.scala
- hlsOptimizerRules.scala
- BGZFCodec.scala
- ComDatabricksDataSource.scala
- ExpectsGenotypeFields.scala
- HadoopLineIterator.scala
- LeveneHaldane.scala
- RowConverter.scala
- SerializableConfiguration.scala
- BigFileDatasource.scala
- GlowConf.scala
- LeftOverlapJoin.scala
- SqlExtensionProvider.scala
- BlockVariantsAndSamplesTransformer.scala
- VariantSampleBlockMaker.scala
- NormalizeVariantsTransformer.scala
- VariantNormalizer.scala
- CleanupPipeTransformer.scala
- Piper.scala
- PipeTransformer.scala
- UTF8TextInputFormatter.scala
- UTF8TextOutputFormatter.scala
- SplitMultiallelicsTransformer.scala
- VariantSplitter.scala
- LiftOverVariantsTransformer.scala
- AnnotationUtils.scala
- BigVCFDatasource.scala
- InternalRowToVariantContextConverter.scala
- LineIteratorImpl.scala
- TabixIndexHelper.scala
- VariantContextToInternalRowConverter.scala
- VCFFileFormat.scala
- VCFFileWriter.scala
- VCFHeaderUtils.scala
- VCFInputFormatter.scala
- VCFLineToInternalRowConverter.scala
- VCFMetadataLoader.scala
- VCFOutputFormatter.scala
- VCFRowHeaderLines.scala
- VCFSchemaInferrer.scala
- VCFStreamWriter.scala
- VCFWriterUtils.scala
- functions.scala
- Glow.scala
- SparkShimBase.scala
- TestAssemblyJar.scala
- QuinaryOptionalExpression.scala
- SenaryExpression.scala
- SQLUtils.scala
- GlowBGZFOutputStream.scala
- StringUtils.scala
- StringUtils.scala
- SparkShim.scala
- SQLUtilsShim.scala
- SparkShim.scala
- SQLUtilsShim.scala
- SparkShim.scala
- SQLUtilsShim.scala
- io.projectglow.DataFrameTransformer
- io.projectglow.sql.BigFileUploader
- io.projectglow.transformers.pipe.InputFormatterFactory
- io.projectglow.transformers.pipe.OutputFormatterFactory
- log4j2.properties
- test-functions.yml
- BgenConverterBaseTest.scala
- BgenReaderSuite.scala
- BgenRowConverterSuite.scala
- BgenWriterSuite.scala
- SimpleIntervalSuite.scala
- TestUtils.scala
- WithUtilsSuite.scala
- GffReaderSuite.scala
- PlinkReaderSuite.scala
- ExpectsGenotypeFieldsSuite.scala
- BigFileDatasourceSuite.scala
- ComDatabricksDataSourceSuite.scala
- GlowBaseTest.scala
- GlowTestData.scala
- LeftOverlapJoinSuite.scala
- SingleFileWriterSuite.scala
- SqlExtensionProviderSuite.scala
- LiftOverCoordinatesExprSuite.scala
- LinearRegressionSuite.scala
- LogisticRegressionSuite.scala
- MomentAggStateSuite.scala
- NewtonIterationsStateSuite.scala
- RegressionTestUtils.scala
- SampleQcExprsSuite.scala
- VariantQcExprsSuite.scala
- VariantUtilExprsSuite.scala
- BlockVariantsAndSamplesTransformerSuite.scala
- NormalizeVariantsTransformerSuite.scala
- VariantNormalizerSuite.scala
- PipeTransformerSuite.scala
- TextPiperSuite.scala
- SplitMultiallelicsTransformerSuite.scala
- VariantSplitterSuite.scala
- StringUtilsSuite.scala
- LiftOverVariantsTransformerSuite.scala
- InternalRowToVariantContextConverterSuite.scala
- TabixHelperSuite.scala
- VariantContextToInternalRowConverterSuite.scala
- VCFConverterBaseTest.scala
- VCFDatasourceSuite.scala
- VCFFileWriterSuite.scala
- VCFHeaderUtilsSuite.scala
- VCFPiperSuite.scala
- VCFSchemaInferrerSuite.scala
- VCFStreamWriterSuite.scala
- GlowSuite.scala
- SparkSuite.scala
- SparkTestShimBase.scala
- QuinaryOptionalExpressionSuite.scala
- GlowGridTest.scala
- SparkTestShim.scala
- GlowGridTest.scala
- SparkTestShim.scala
- GlowGridTest.scala
- SparkTestShim.scala
- SQLUtilsShimSuite.scala
- functions.scala.TEMPLATE
- build
- gen-nb-src.py
- multitask-integration-test-config.json
- run-nb-test.py
- notebook.py
- glow.css
- Dockerfile
- blockmatrix.png
- databricks_container_services_admin_console.png
- glow-repo-notebooks.png
- glow_ci_pipeline.png
- glow_databricks_container_services_cluster_config.png
- glow_gwas_tutorial_run.png
- glow_ref_arch_genomics.png
- wgr_diagram.png
- wgr_runtime.png
- download_1000G.html
- functions.html
- 10_liftOver.html
- 1_simulate_covariates_phenotypes_offset.html
- 2_simulate_delta_pvcf.html
- 3_delta_to_vcf.html
- 6_explode_variant_dataframe.html
- 7_etl_gff_annotations.html
- 8_create_database_for_querying.html
- 9_query_variant_db.html
- merge-vcf.html
- normalizevariants.html
- sample-qc-demo.html
- splitmultiallelics-transformer.html
- variant-data.html
- variant-qc-demo.html
- vcf2delta.html
- 0_ingest_vcf2delta.html
- 1_quality_control.html
- 2_quantitative_glowgr.html
- 3_linear_gwas_glow.html
- 4_binary_glowgr.html
- 5_logistic_gwas_glow.html
- 8_pipeline_runs_comparison.html
- binaryglowgr.html
- glowgr.html
- gwas-binary.html
- gwas-quantitative.html
- pandas-lmm.html
- parallel_bcftools_filter.html
- pipe-transformer-plink.html
- pipe-transformer-vep.html
- pipe-transformer.html
- 0_setup_constants_glow.html
- 2_setup_metadata.html
- download_1000G.py
- functions.py
- 10_liftOver.py
- 1_simulate_covariates_phenotypes_offset.py
- 2_simulate_delta_pvcf.py
- 3_delta_to_vcf.py
- 4_vcf_to_hail_mt.py
- 5_hail_mt_to_glow.py
- 6_explode_variant_dataframe.py
- 7_etl_gff_annotations.py
- 8_create_database_for_querying.py
- 9_query_variant_db.py
- hail-interoperation.py
- merge-vcf.py
- normalizevariants.py
- sample-qc-demo.py
- splitmultiallelics-transformer.py
- variant-data.py
- variant-qc-demo.py
- vcf2delta.py
- 0_ingest_vcf2delta.py
- 1_quality_control.py
- 2_quantitative_glowgr.py
- 3_linear_gwas_glow.py
- 4_binary_glowgr.py
- 5_logistic_gwas_glow.py
- 6_hail_linreg_gwas.py
- 7_hail_logistic_gwas.py
- 8_pipeline_runs_comparison.py
- 9_compare_hail_to_glow.py
- binaryglowgr.py
- glowgr.py
- gwas-binary.py
- gwas-quantitative.py
- pandas-lmm.py
- parallel_bcftools_filter.py
- pipe-transformer-plink.py
- pipe-transformer-vep.py
- pipe-transformer.py
- 0_setup_constants_glow.py
- 1_setup_constants_hail.py
- 2_setup_metadata.py
- attach-mlflow.gif
- community-edition.rst
- import-dbc.gif
- index.rst
- glowgr.rst
- index.rst
- pyspark-functions.rst
- toplevel-functions.rst
- fig1.png
- fig2.png
- fig3.png
- fig4.png
- fig5.png
- glowgr-blog.rst
- figcsqdf.png
- fignormdf.png
- fignormnorepdf.png
- figorigdf.png
- figsplitdf.png
- release-0-3-0-blog.rst
- annotations_df.png
- gene_transcript_df.png
- parent_child_df.png
- release-0-4-0-blog.rst
- transcript_exon_df.png
- variant_exon_transcript_gene_df.png
- variants_df.png
- figflowchartglow.png
- figleftalign.png
- fignormalizeddf.png
- figoriginaldf.png
- figparsimony.png
- figsplitnormalizeddf.png
- variant-normalization-blog.rst
- index.rst
- custom-patches.rst
- databricks-environment.rst
- index.rst
- data-simulation.rst
- gff.rst
- index.rst
- lift-over.rst
- merge.rst
- sample-qc.rst
- utility-functions.rst
- variant-data.rst
- variant-normalization.rst
- variant-qc.rst
- variant-splitter.rst
- vcf2delta.rst
- index.rst
- pandas-udf.rst
- pipe-transformer.rst
- regression-tests.rst
- whole-genome-regression.rst
- conf.py
- conftest.py
- contributing.rst
- environment.yml
- getting-started.rst
- index.rst
- introduction.rst
- troubleshooting.rst
- tutorial.rst
- make.bat
- Makefile
- README.md
- Dockerfile
- build.properties
- Dependencies.scala
- plugins.sbt
- functions.py
- test_approx_firth.py
- test_lin_reg.py
- test_log_reg.py
- __init__.py
- approx_firth.py
- functions.py
- lin_reg.py
- log_reg.py
- __init__.py
- hlseventlogger.py
- __init__.py
- test_overlap_join.py
- __init__.py
- functions.py
- __init__.py
- test_conversions.py
- test_register.py
- test_transform.py
- __init__.py
- test_block_variants_and_samples.py
- test_estimate_loco_offsets.py
- test_functions.py
- test_logistic_ridge_regression.py
- test_reshape_for_gwas.py
- test_ridge_regression.py
- test_sample_id_extraction.py
- __init__.py
- logistic_ridge_regression.py
- logistic_udfs.py
- model_functions.py
- ridge_reduction.py
- ridge_regression.py
- ridge_udfs.py
- wgr_functions.py
- __init__.py
- conftest.py
- conversions.py
- functions.py
- functions.py.TEMPLATE
- glow.py
- build.properties
- .style.yapf
- environment.yml
- LICENSE.txt
- MANIFEST.in
- README.rst
- render_template.py
- setup.py
- spark-4-environment.yml
- test_render_template.py
- version.py
- favicon.ico
- glow_genomics_docker_image_architecture.png
- glow_logo_horiz_color.png
- glow_logo_horiz_color_dark_bg.png
- glow_logo_small.png
- intersect_21.bed
- .index.crc
- .metadata.json.gz.crc
- index
- metadata.json.gz
- .index.crc
- .metadata.json.gz.crc
- index
- metadata.json.gz
- complex.16bits.bgen
- complex.16bits.threshold-0.9.vcf
- complex.16bits.vcf
- example.16bits.bgen
- example.16bits.bgen.bgi
- example.16bits.noindex.bgen
- example.16bits.nosampleids.bgen
- example.16bits.oxford.bgen
- example.16bits.oxford.corrupted.sample
- example.16bits.oxford.sample
- example.16bits.threshold-0.9.vcf
- example.16bits.threshold-0.95.vcf
- example.16bits.vcf
- example.32bits.bgen
- example.32bits.vcf
- example.3bits.bgen
- example.8bits.bgen
- example.8bits.uncompressed.bgen
- example.8bits.vcf
- example.8bits.zstd.bgen
- example.fake.sample
- example.sample
- phased.16bits.bgen
- phased.16bits.threshold-0.9.vcf
- phased.16bits.vcf
- phased.8bits.bgen
- phased.8bits.vcf
- README.md
- test_gff_empty.gff
- test_gff_with_fasta.gff
- test_gff_with_fasta.gff.bgz
- test_gff_with_fasta.gff.gz
- test_gff_with_fasta_bgzip.gff.gz
- test_gff_with_fasta_multicase_attribute.gff
- binary-offsets.csv.gz
- binary-phenotypes.csv.gz
- continuous-offsets.csv.gz
- continuous-phenotypes.csv.gz
- covariates.csv.gz
- genotypes.vcf.gz
- README
- dummy.reference.dict
- dummy.reference.fasta
- dummy.two.block.reference.dict
- dummy.two.block.reference.fasta
- dummy2.reference.dict
- dummy2.reference.fasta
- failed.mismatchRefSeq.testLiftoverBiallelicIndels.vcf
- failed.testLiftoverBiallelicIndels.vcf
- failed.testLiftoverIndelFlip.vcf
- failed.testLiftoverIndelNoFlip.vcf
- failed.testLiftoverMultiallelicIndels.vcf
- failed.testLiftoverSwapRefAltVariants.vcf
- lifted.mismatchRefSeq.testLiftoverBiallelicIndels.vcf
- lifted.testLiftoverBiallelicIndels.vcf
- lifted.testLiftoverIndelFlip.vcf
- lifted.testLiftoverIndelNoFlip.vcf
- lifted.testLiftoverMultiallelicIndels.vcf
- lifted.testLiftoverSwapRefAltVariants.vcf
- mini.reference.dict
- mini.reference.fasta
- test.over.chain
- test.two.block.over.chain
- testLiftoverBiallelicIndels.vcf
- testLiftoverIndelFlip.vcf
- testLiftoverIndelNoFlip.vcf
- testLiftoverMismatchingSnps.vcf
- testLiftoverMultiallelicIndels.vcf
- testLiftoverSwapRefAltVariants.vcf
- testLiftoverUsingMissingContig.vcf
- failed.combined.chr20_18210071_18210093.g.vcf
- failed.minMatch001.test.bed
- failed.minMatch05.test.bed
- failed.swapRefAltAndArrays.vcf
- failed.test.vcf
- hg19.chr20.dict
- hg19.chr20.fa.gz
- hg38ToHg19.over.chain.gz
- lifted.combined.chr20_18210071_18210093.g.vcf
- lifted.minMatch001.test.bed
- lifted.minMatch05.test.bed
- lifted.swapRefAltAndArrays.vcf
- lifted.test.vcf
- README
- unlifted.swapRefAltAndArrays.vcf
- unlifted.test.bed
- unlifted.test.vcf
- test.bed
- test.bim
- test.fam
- test.bed
- test.bim
- test.fam
- test.map
- test.ped
- test.bed
- test.fam
- test.bed
- test.bim
- test.vcf
- README
- binarywithoffset.txt
- sex2withoffset.txt
- covariates.txt
- example.bgen
- example_3chr.bgen
- example_3chr.bgen.bgi
- example_3chr.sample
- fit_bin_out.log
- fit_bin_out_1.loco
- fit_bin_out_2.loco
- fit_bin_out_pred.list
- fit_lin_out.log
- fit_lin_out_1.loco
- fit_lin_out_2.loco
- fit_lin_out_3chr_1.loco
- fit_lin_out_3chr_2.loco
- fit_lin_out_3chr_pred.list
- fit_lin_out_pred.list
- phenotype.txt
- phenotype_bin.txt
- test_bin_out_firth.log
- test_bin_out_firth_Y1.regenie
- test_bin_out_firth_Y2.regenie
- test_bin_out_half_firth.log
- test_bin_out_half_firth_Y1.regenie
- test_bin_out_half_firth_Y2.regenie
- test_bin_out_missing_firth.log
- test_bin_out_missing_firth_Y1.regenie
- test_bin_out_missing_firth_Y2.regenie
- test_lin_out.log
- test_lin_out_3chr_Y1.regenie
- test_lin_out_3chr_Y2.regenie
- test_lin_out_missing_Y1.regenie
- test_lin_out_missing_Y2.regenie
- test_lin_out_Y1.regenie
- test_lin_out_Y2.regenie
- 1000G.phase3.broad.withGenotypes.chr20.10100000.vcf.gz
- 1000G.phase3.broad.withGenotypes.chr20.10100000.vcf.gz.tbi
- CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf.gz
- CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf.gz.tbi
- combined.chr20_18210071_18210093.g.vcf.gz
- combined.chr20_18210071_18210093.g.vcf.gz.tbi
- NA12878_21_10002403.vcf.gz
- NA12878_21_10002403.vcf.gz.tbi
- NA12878_21_10002403NoTbi.vcf.gz
- 1000G.phase3.broad.withGenotypes.chr20.10100000.100Samples.Blocked.tsv
- README
- 01_IN_altered_biallelic.vcf
- 01_IN_altered_biallelic_bcftoolsnormalized.vcf
- 01_IN_altered_biallelic_vtdecompose.vcf
- 01_IN_altered_biallelic_vtdecompose_bcftoolsnormalized.vcf
- 01_IN_altered_multiallelic.vcf
- 01_IN_altered_multiallelic_bcftoolsnormalized.vcf
- 01_IN_altered_multiallelic_vtdecompose.vcf
- 01_IN_altered_multiallelic_vtdecompose_bcftoolsnormalized.vcf
- 20_altered.fasta
- 20_altered.fasta.fai
- 20_altered_bgzip.fasta.gz
- 20_altered_bgzip.fasta.gz.fai
- 20_altered_bgzip.fasta.gz.gzi
- 20_altered_bgzip_noindex.fasta.gz
- 20_altered_noindex.fasta
- Homo_sapiens_assembly38.20.21_altered.fasta
- Homo_sapiens_assembly38.20.21_altered.fasta.fai
- test_left_align_hg38_altered.vcf
- test_left_align_hg38_altered_bcftoolsnormalized.vcf
- test_left_align_hg38_altered_symbolic.vcf
- test_left_align_hg38_altered_symbolic_bcftoolsnormalized.vcf
- test_left_align_hg38_altered_symbolic_vtdecompose.vcf
- test_left_align_hg38_altered_symbolic_vtdecompose_bcftoolsnormalized.vcf
- test_left_align_hg38_altered_vtdecompose.vcf
- test_left_align_hg38_altered_vtdecompose_bcftoolsnormalized.vcf
- group_file.txt
- gwas-region.py
- gwas.sh
- prepend-chr.sh
- remove-info.sh
- remove-rows.sh
- 1row.vcf.bgz
- 1row_bgz.vcf.gz
- 1row_not_bgz.vcf.gz
- loftee.vcf
- misnumbered_info.vcf
- missing_contig_length.vcf
- snpeff.vcf
- test_withInfGenotype.vcf
- test_withInfQual.vcf
- test_withNanGenotype.vcf
- test_withNanQual.vcf
- VCFv4.3.vcf
- vep.vcf
- HG00096.vcf.bgz
- HG00097.vcf.bgz
- README.txt
- binary_phenotypes.csv
- bt_reduceded_1part.snappy.parquet
- cov.csv
- groupedIDs.snappy.parquet
- test_logistic_regression_fit.json
- test_logistic_regression_predict_proba.json
- test_logistic_regression_transform.json
- test_map_irls_eqn.json
- test_reduce_irls_eqn.json
- test_score_logistic_model.json
- test_solve_irls_eqn.json
- blockedGT.snappy.parquet
- groupedIDs.snappy.parquet
- level1BlockedGT.snappy.parquet
- level1YHatLoco.csv
- level2BlockedGT.snappy.parquet
- level2YHatLoco.csv
- pts.csv
- README.md
- X0.csv
- X1.csv
- X2.csv
- 1000G.phase3.broad.withGenotypes.chr20.10100000.vcf
- 1000genomes-phase3-1row.vcf
- 1kg_sample with spaces.vcf
- 1kg_sample.vcf
- biallelic.CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf
- CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf
- combined.chr20_18210071_18210093.g.vcf
- NA12878_21_10002403.bp.g.vcf
- NA12878_21_10002403.g.vcf
- NA12878_21_10002403.vcf
- no_header.csv
- saige_output.txt
- test.chr17.vcf
- .git-blame-ignore-revs
- .gitignore
- .readthedocs.yml
- .scala-steward.conf
- .scalafmt.conf
- build.sbt
- CODE-OF-CONDUCT.md
- codecov.yml
- conftest.py
- CONTRIBUTING.md
- functions.yml
- GIT-PROCESS.md
- identity.py
- levels_ridge_regression_tutorial.ipynb
- LICENSE.txt
- pyspark-setup.py
- pytest.ini
- README.md
- RELEASE.md
- scalastyle-config.xml
- sonatype.sbt
- stable-version.txt
- version.sbt
# Installation Guide
1. Get the code
git clone https://github.com/projectglow/glow
Downloads the entire project code from GitHub to your computer.
cd glow
Moves into the project folder you just downloaded.
2. Python
Easy RecommendedPrerequisites
pip install .
Installs the package published on PyPI directly β no need to clone the source.
jupyter notebook
Launches Jupyter in your browser so you can open and run the notebook (.ipynb) files.
If it runs without errors and prints output in the terminal, it worked.
// repository documentation
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