VCFLEFTALIGN(1)

NAME

vcfleftalign

SYNOPSIS

vcfleftalign options [file]

DESCRIPTION

Left-align indels and complex variants in the input using a pairwise ref/alt alignment followed by a heuristic, iterative left realignment process that shifts indel representations to their absolute leftmost (5’) extent.

OPTIONS

    This is the same procedure used in the internal left alignment in
    freebayes, and can be used when preparing VCF files for input to
    freebayes to decrease positional representation differences between
    the input alleles and left-realigned alignments.
    options:
            -r, --reference FILE  Use this reference as a basis for realignment.
            -w, --window N        Use a window of this many bp when left aligning (150).
    Left-aligns variants in the specified input file or stdin.  Window
    size is determined dynamically according to the entropy of the regions
    flanking the indel.  These must have entropy > 1 bit/bp, or be shorter
    than ~5kb.
    Type: transformation

EXIT VALUES

0   Success

not 0
    Failure

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS
Erik Garrison and vcflib contributors.