---
name: "vcfleftalign"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcfleftalign"
---

# 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)](/vcflib/1.md)

## OTHER

## LICENSE

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

## AUTHORS

Erik Garrison and vcflib contributors.