vcfutils-pl

name	vcfutils-pl
description	Use when working with VCF file utilities from the bcftools bioconda package.
disable-model-invocation	true
user-invocable	true

vcfutils-pl

Quick Start

• Command: vcfutils.pl <command> [arguments]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcfutils.pl
• Reference: See references/help.md for detailed usage

When To Use This Tool

• Run legacy VCF helper subcommands bundled with the bcftools toolchain.
• Subset samples, list sample names, or fill AC/AN counts in VCF records.
• Compute quick quality statistics or apply the legacy varFilter.
• Convert all-site VCF output into consensus FASTQ with vcf2fq.

Common Patterns

# 1) List sample names in a VCF
vcfutils.pl \
  listsam \
  cohort.vcf

# 2) Fill AC/AN fields from genotypes
vcfutils.pl \
  fillac \
  cohort.vcf \
  > cohort.with-ac.vcf

# 3) Apply the legacy short-variant filter helper
vcfutils.pl \
  varFilter \
  cohort.vcf \
  > cohort.filtered.vcf

# 4) Build a consensus FASTQ from an all-site VCF
vcfutils.pl \
  vcf2fq \
  all-sites.vcf \
  > consensus.fq

Recommended Workflow

1. Start by choosing the subcommand that matches the task, because vcfutils.pl is a command multiplexer rather than a single-purpose tool.
2. Validate whether the chosen subcommand expects ordinary VCF input, an all-site VCF, a .fai, or bcftools-specific annotations.
3. Run the subcommand and redirect output into a new file, because most modes write transformed text to stdout.
4. Re-validate the resulting VCF/FASTQ before plugging it into downstream analysis.

Guardrails

• The first argument must be a subcommand such as listsam, fillac, qstats, varFilter, or vcf2fq; -h, --help, and --version are not valid top-level help flags.
• fillac expects the GT field to be present and to appear first in the FORMAT column.
• vcf2fq is intended for all-site, position-sorted VCF input and will complain about unsorted data.
• varFilter and some related commands rely on annotations produced by the SAMtools/BCFtools legacy calling pipeline.