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‎dist/igsr_analysis-1.0.1.tar.gz

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‎igsr_analysis.egg-info/PKG-INFO

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Metadata-Version: 2.1
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Name: igsr-analysis
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Version: 1.0.1
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Summary: This package contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data.
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Home-page: https://github.com/igsr/igsr_analysis/archive/refs/tags/v1.0.1.tar.gz
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Author: Ernesto Lowy
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Author-email: [email protected]
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License: MIT
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Description:
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This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data
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The International Genome Sample Resource [(IGSR)](http://www.internationalgenome.org/) is a project funded by the [Wellcome Trust](https://wellcome.ac.uk/) created after the finalization of the 1000 Genomes Project in order to maintain and expand the resource. It has the following aims:
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* Ensure the future access to and usability of the 1000 Genomes reference data
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* Incorporate additional published genomic data on the 1000 Genomes samples
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* Expand the data collection to include new populations not represented in the 1000 Genomes Project
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This repository contains code used in the different analyses pipelines that we use in the project. To use this code please follow the steps described below
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### Preparing environment
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Modify your $PYTHONPATH to include the required libraries:<br>
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```export PYTHONPATH=${ehive_dir}/wrappers/python3/:$PYTHONPATH```
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Modify your $PERL5LIB to include the required libraries:<br>
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```export PERL5LIB=${ehive_dir}/modules/:${igsr_analysis_dir}/:${PERL5LIB}```
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Modify your $PATH to include the location of the eHive scripts:
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```export PATH=${ehive_dir}/scripts/:${PATH}```
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### Install the igsr_analysis package from PyPI
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```pip install igsr_analysis```
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And you are ready to go!
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### Conventions used in this README file:
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```${igsr_analysis_dir}``` is the folder where you have cloned https://github.com/igsr/igsr_analysis.git<br>
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```${ehive_dir}``` is the folder where you have cloned https://github.com/Ensembl/ensembl-hive.git<br>
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[![DOI](https://zenodo.org/badge/99792445.svg)](https://zenodo.org/badge/latestdoi/99792445)
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Platform: UNKNOWN
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.0
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Classifier: Programming Language :: Python :: Implementation :: CPython
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Classifier: Programming Language :: Python :: Implementation :: PyPy
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Requires-Python: >=3.0.0
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Description-Content-Type: text/markdown

‎igsr_analysis.egg-info/SOURCES.txt

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README.md
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setup.py
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BEDTools/BEDTools.py
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BEDTools/__init__.py
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BamQC/BamQC.py
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BamQC/__init__.py
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PyHive/Hive.py
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PyHive/__init__.py
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PyHive/Attribute/StoreAttribute.py
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PyHive/Attribute/__init__.py
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PyHive/Bam/RunSamToolsIndex.py
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PyHive/Bam/RunSamToolsMerge.py
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PyHive/Bam/__init__.py
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PyHive/BamQC/RunChkIndelRg.py
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PyHive/BamQC/RunPicardOnWESfile.py
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PyHive/BamQC/RunPicardOnWGSfile.py
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PyHive/BamQC/RunVerifyBamId.py
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PyHive/BamQC/__init__.py
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PyHive/Factories/BeagleChunkFactory.py
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PyHive/Factories/ChrFactory.py
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PyHive/Factories/CoordFactory.py
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PyHive/Factories/ShapeitChunkFactory.py
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PyHive/Factories/SliceFactory.py
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PyHive/Factories/SplitVCF.py
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PyHive/Factories/SplitVCFintoChros.py
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PyHive/Factories/TransposeBam.py
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PyHive/Factories/__init__.py
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PyHive/File/CompressBybgzip.py
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PyHive/File/ShortenFilePaths.py
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PyHive/File/ShortenFiles.py
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PyHive/File/SplitFile.py
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PyHive/File/StoreFile.py
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PyHive/File/__init__.py
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PyHive/Seed/SeedFile.py
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PyHive/Seed/SeedShapeit.py
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PyHive/Seed/SeedVCFIntegration.py
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PyHive/Seed/__init__.py
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PyHive/TOPMed/IndexBam.py
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PyHive/TOPMed/MarkDuplicates.py
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PyHive/TOPMed/RnaseqcCounts.py
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PyHive/TOPMed/Rsem.py
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PyHive/TOPMed/SamtoolsQuickcheck.py
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PyHive/TOPMed/Star.py
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PyHive/TOPMed/__init__.py
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PyHive/VariantCalling/BCFTools_caller.py
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PyHive/VariantCalling/GATK_HC.py
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PyHive/VariantCalling/GATK_UG.py
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PyHive/VariantCalling/__init__.py
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PyHive/Vcf/BcftoolsVcfNorm.py
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PyHive/Vcf/CombineVariants.py
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PyHive/Vcf/NormVcf.py
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PyHive/Vcf/VariantsToAllelicPrimitives.py
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PyHive/Vcf/VcfAllelicPrim.py
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PyHive/Vcf/VcfCombine.py
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PyHive/Vcf/VcfConcat.py
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PyHive/Vcf/VcfIxByTabix.py
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PyHive/Vcf/VcfReheader.py
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PyHive/Vcf/VcfReplaceChrNames.py
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PyHive/Vcf/__init__.py
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PyHive/Vcf/convertPL2GL.py
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PyHive/Vcf/dropInfo.py
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PyHive/VcfFilter/ApplyRecalibration.py
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PyHive/VcfFilter/BcftoolsFilter.py
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PyHive/VcfFilter/SelectVariants.py
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PyHive/VcfFilter/SplitVariants.py
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PyHive/VcfFilter/SubsetVcfWithBed.py
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PyHive/VcfFilter/SubsetVcfWithRegion.py
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PyHive/VcfFilter/VariantRecalibrator.py
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PyHive/VcfFilter/__init__.py
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PyHive/VcfIntegration/CollectRawF.py
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PyHive/VcfIntegration/SNPTools_bamodel.py
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PyHive/VcfIntegration/SNPTools_poprob.py
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PyHive/VcfIntegration/SNPTools_prob2vcf.py
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PyHive/VcfIntegration/__init__.py
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PyHive/VcfIntegration/run_Beagle.py
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PyHive/VcfIntegration/run_Shapeit.py
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PyHive/VcfIntegration/run_Shapeit_convert2vcf.py
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PyHive/VcfIntegration/run_ligateHAPLOTYPES.py
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PyHive/VcfIntegration/run_prepareGenFromBeagle4.py
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PyHive/VcfQC/BcftoolsStats.py
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PyHive/VcfQC/ChrosInVcf.py
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PyHive/VcfQC/CollectVariantCallingMetrics.py
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PyHive/VcfQC/GTConcordance.py
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PyHive/VcfQC/PlotVariantDensity.py
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PyHive/VcfQC/VariantsInRegions.py
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PyHive/VcfQC/__init__.py
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ReseqTrackDB/ReseqTrackDB.py
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ReseqTrackDB/__init__.py
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ReseqTrackDB/main.py
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SequenceIndex/SequenceIndex.py
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SequenceIndex/__init__.py
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SequenceIndex/main.py
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Utils/RunProgram.py
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Utils/RunSingularity.py
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Utils/__init__.py
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VCF/VcfNormalize.py
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VCF/VcfQC.py
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VCF/VcfUtils.py
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VCF/__init__.py
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VCF/VCFIntegration/Beagle.py
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VCF/VCFIntegration/SNPTools.py
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VCF/VCFIntegration/Shapeit.py
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VCF/VCFIntegration/__init__.py
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VCF/VCFfilter/BCFTools.py
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VCF/VCFfilter/GATK.py
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VCF/VCFfilter/MLclassifier.py
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VCF/VCFfilter/__init__.py
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VariantCalling/BCFTools.py
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VariantCalling/GATK.py
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VariantCalling/__init__.py
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igsr_analysis.egg-info/PKG-INFO
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igsr_analysis.egg-info/SOURCES.txt
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igsr_analysis.egg-info/dependency_links.txt
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igsr_analysis.egg-info/requires.txt
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igsr_analysis.egg-info/top_level.txt
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p3/__init__.py
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p3/p3BAMQC.py

‎igsr_analysis.egg-info/dependency_links.txt

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‎igsr_analysis.egg-info/requires.txt

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pandas

‎igsr_analysis.egg-info/top_level.txt

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BEDTools
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BamQC
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PyHive
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ReseqTrackDB
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SequenceIndex
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Utils
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VCF
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VariantCalling
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p3

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