Provided by: libvcflib-tools_1.0.3+dfsg-1_amd64 bug

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.