Package org.broadinstitute.hellbender.tools.walkers.fasta

package org.broadinstitute.hellbender.tools.walkers.fasta
  • Classes
    Class
    Description
    CountBasesInReference
    Counts the number of times each base occurs in a reference, and prints the counts to standard output (and optionally to a file).
    FastaAlternateReferenceMaker
    Generate an alternative reference sequence over the specified interval
    FastaReferenceMaker
    Create a subset of a FASTA reference sequence
    ShiftFasta
    Create a fasta with the bases shifted by offset delta1 = offset - 1 delta2 = total - delta1 To shift forward: if you are given a position in the regular fasta (pos_r) and want the position in the shifted fasta (pos_s): if pos_r > delta1 => pos_s = pos_r - delta1 == pos_r - offset +1 otherwise pos_s = pos_r + delta2 == pos_r + total - offset + 1 To shift back: if you are given a position in the shifted fasta (pos_s) and want the position in the regular fasta (pos_r): if pos_s > delta2 => pos_r = pos_s - delta2 == pos_s - total + offset - 1 otherwise pos_r = pos_s + delta1 == pos_s + offset - 1 Example command line: ShiftFasta -R "<CIRCURLAR_REFERENCE.fasta>" // the reference to shift -O "<SHIFTED_REFERENCE.fasta>" // output; the shifted fasta --shift-back-output "<SHIFT_BACK.chain>" // output; the shiftback chain file to use when lifting over --shift-offset-list "" // optional; Specifies the offset to shift for each contig in the reference.