GitHub - AshKernow/VariantFilterScripts

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Name		Name	Last commit message	Last commit date
Latest commit History 68 Commits
.gitignore		.gitignore
CountGenotypes.py		CountGenotypes.py
ExmFilt.1.FilterbyAlleleFrequency.py		ExmFilt.1.FilterbyAlleleFrequency.py
ExmFilt.2.DeleteriousAlternateAllele.py		ExmFilt.2.DeleteriousAlternateAllele.py
ExmFilt.3.AlternateAlleleFilter.py		ExmFilt.3.AlternateAlleleFilter.py
ExmFilt.4.VCFtoTable.py		ExmFilt.4.VCFtoTable.py
ExmFilt.4.VCFtoTable_FullInfo.py		ExmFilt.4.VCFtoTable_FullInfo.py
ExmFilt.5.VCFtoFamilies.sh		ExmFilt.5.VCFtoFamilies.sh
ExmFilt.CustomGenotype.py		ExmFilt.CustomGenotype.py
ExmFilt.CustomGenotype_with_Table.py		ExmFilt.CustomGenotype_with_Table.py
ExmFilt.GetSpecificGeneInFamily.py		ExmFilt.GetSpecificGeneInFamily.py
README		README
xAnnotateVariantTSV.sh		xAnnotateVariantTSV.sh
xCompoundHetFilters.sh		xCompoundHetFilters.sh
xContrastTwins.sh		xContrastTwins.sh
xExmCheckKinship.sh		xExmCheckKinship.sh
xFamilyFilters.sh		xFamilyFilters.sh
xGetCompoundHet.sh		xGetCompoundHet.sh
xIndividualcHet.sh		xIndividualcHet.sh
xProbandParentFilters.sh		xProbandParentFilters.sh
xSingletonFilters.sh		xSingletonFilters.sh
xTrioFilters.sh		xTrioFilters.sh
xTrioFilters_table.sh		xTrioFilters_table.sh

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The scripts are used to filter variants according to different inheritance models. The base python script filters a vcf file using the genotypes of provided individuals, allele frequencies, and various quality metrics. The bash scripts are wrappers that apply the custom filtering python script for different pedigree types.