vcfleftalign

Authors

       Erik Garrison and vcflib contributors.

vcfleftalign (vcflib)                                                                            VCFLEFTALIGN(1)

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  left‐
       most (5’) extent.

Exit Values

0      Success

       not0  Failure

License

       Copyright  2011-2024  (C)  Erik Garrison and vcflib contributors.  MIT licensed.  Copyright 2020-2024 (C)
       Pjotr Prins.

Name

vcfleftalign

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