Package org.broadinstitute.hellbender.tools.walkers.consensus

package org.broadinstitute.hellbender.tools.walkers.consensus
  • Classes
    Class
    Description
    DownsampleByDuplicateSet
    Given a bam grouped by the same unique molecular identifier (UMI), this tool drops a specified fraction of duplicate sets and returns a new bam.
    MoleculeID
    A container class for the molecule ID, which consists of an integer ID and a binary strand.
    ReadsWithSameUMI
    A container class for a set of reads that share the same unique molecular identifier (UMI) as judged by FGBio GroupReadsByUmi (http://fulcrumgenomics.github.io/fgbio/tools/latest/GroupReadsByUmi.html) Examples of molecule IDs (MI tag): "0/A" (The first molecule in the bam, A strand) "0/B" (The first molecule in the bam, B strand) "99/A" (100th molecule in the bam, A strand) For a given set of reads with the same molecule number, the strand with a larger number of reads is defined as the A strand.