Package org.broadinstitute.hellbender.tools.funcotator.filtrationRules
package org.broadinstitute.hellbender.tools.funcotator.filtrationRules
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ClassesClassDescriptionAllele frequency calculations for the Exac datasetAllele frequency utilities that are dataset-agnostic
FuncotationFiltermatching variants which: Occur on a gene in the American College of Medical Genomics (ACMG)'s list of clinically-significant variants Have been labeled by ClinVar as pathogenic or likely pathogenic Have a max MAF of 5% across sub-populations of ExAC or gnomADA filter to apply to Funcotations inFilterFuncotations.FuncotationFiltermatching variants which: Have been flagged by LMM as important for loss of function.FuncotationFiltermatching variants which: Are classified as FRAME_SHIFT_*, NONSENSE, START_CODON_DEL, or SPLICE_SITE Occur on a gene where loss of function is a disease mechanism Have a max MAF of 1% across sub-populations of ExAC or gnomAD