Package org.broadinstitute.hellbender.tools.walkers.mutect.filtering
package org.broadinstitute.hellbender.tools.walkers.mutect.filtering
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ClassDescriptionHelps read and set allele specific filters in the INFO field.Errors in Mutect2 fall into three major categories -- technical artifacts that depend on (usually hidden) features and do not follow the independent reads assumption of the somatic likelihoods model, non-somatic variants such as germline mutations and contamination, and sequencing errors that are captured by the base qualities and the somatic likelihoods model.Helper class used on the final pass of
FilterMutectCallsto record total expected true positives, false positives, and false negatives, as well as false positives and false negatives attributable to each filterFilter variants in a Mutect2 VCF callset.Base class for Hard filters that are applied at the allele levelBase class for filters that apply at the allele level.Base class for all Mutect2Filters