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

# vcffixup(1)

## NAME

**vcffixup**

## SYNOPSIS

**vcffixup**

## DESCRIPTION

Generates a VCF stream where AC and NS have been generated for each record using sample genotypes

## OPTIONS

-

  ```
  Count the allele frequencies across alleles present in each record in the VCF file. (Similar to vcftools --freq.)
  Uses genotypes from the VCF file to correct AC (alternate allele count), AF
  (alternate allele frequency), NS (number of called), in the VCF records.  For
  example:
      % vcfkeepsamples file.vcf NA12878 | **vcffixup** - | vcffilter -f "AC > 0"
  Would downsample file.vcf to only NA12878, removing sites for which the sample
  was not called as polymorphic.
  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.