Vcfutils Pl

# 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.