---
name: "vcf-fix-ploidy"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf-fix-ploidy"
---

# vcf-fix-ploidy(1)

vcf-fix-ploidy

## NAME

vcf-fix-ploidy - vcf-fix-ploidy

## SYNOPSIS

**cat** *broken.vcf \| vcf-fix-ploidy* \[*OPTIONS*\] *\> fixed.vcf*

## OPTIONS

- **-a**, **--assumed-sex** \<sex\>

  M or F, required if the list is not complete in **-s**

- **-l**, **--fix-likelihoods**

  Add or remove het likelihoods (not the default behaviour)

- **-p**, **--ploidy** \<file\>

  Ploidy definition. The default is shown below.

- **-s**, **--samples** \<file\>

  List of sample sexes (sample\_name \[MF\]).

- **-h**, -?, **--help**

  This help message.

### Default ploidy definition:

-

  ploidy =\> {

-

  X =\> \[

-

  \# The pseudoautosomal regions 60,001-2,699,520 and 154,931,044-155,270,560 with the ploidy 2 { from=\>1, to=\>60\_000, M=\>1 }, { from=\>2\_699\_521, to=\>154\_931\_043, M=\>1 },

-

  \], Y =\> \[

-

  \# No chrY in females and one copy in males { from=\>1, to=\>59\_373\_566, M=\>1, F=\>0 },

-

  \], MT =\> \[

-

  \# Haploid MT in males and females { from=\>1, to =\> 16\_569, M=\>1, F=\>1 },

-

  \],

-

  }