vcf-fix-ploidy

name	vcf-fix-ploidy
description	Use when VCF files have incorrect ploidy annotations for sex chromosomes or mitochondrial DNA, particularly when processing samples with known sex but mismatched genotype fields.
disable-model-invocation	true
user-invocable	true

vcf-fix-ploidy

Quick Start

• Command: cat input.vcf | vcf-fix-ploidy [OPTIONS] > output.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-fix-ploidy
• Full reference: See references/help.md

When To Use This Tool

• Repair genotype ploidy for sex chromosomes and mitochondrial DNA after a caller emitted inconsistent diploid-style genotypes.
• Adjust male/female expectations on X, Y, and MT using either a sample-sex file or an assumed default.
• Optionally fix genotype likelihood vectors to match the corrected ploidy.

Common Patterns

# 1) Fix ploidy using a sample-sex file
cat input.vcf \
  | vcf-fix-ploidy -s samples.txt \
  > fixed.vcf

# 2) Assume female sex for unspecified samples
cat input.vcf \
  | vcf-fix-ploidy -s samples.txt -a F \
  > fixed.vcf

# 3) Also adjust genotype likelihoods
cat input.vcf \
  | vcf-fix-ploidy -s samples.txt -l \
  > fixed.vcf

Recommended Workflow

1. Prepare a sample-sex file with one sample_name [M|F] pair per line.
2. Decide whether the default ploidy rules match your reference build and sex-chromosome conventions.
3. Stream the VCF through vcf-fix-ploidy, adding -a if the sex list is incomplete.
4. Validate a few representative X, Y, and MT records before propagating the fixed file further.

Guardrails

• Input is stdin-driven; do not try to pass the VCF as a positional filename.
• If -s is incomplete, you need -a to define the assumed sex for missing samples.
• The built-in ploidy rules are reference- and convention-specific; override them with -p if your build differs.
• -l/--fix-likelihoods changes more than the GT field, so only use it when downstream tools care about PL/GL consistency.