| 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
vcfutils.pl \
listsam \
cohort.vcf
vcfutils.pl \
fillac \
cohort.vcf \
> cohort.with-ac.vcf
vcfutils.pl \
varFilter \
cohort.vcf \
> cohort.filtered.vcf
vcfutils.pl \
vcf2fq \
all-sites.vcf \
> consensus.fq
Recommended Workflow
- Start by choosing the subcommand that matches the task, because
vcfutils.pl is a command multiplexer rather than a single-purpose tool.
- Validate whether the chosen subcommand expects ordinary VCF input, an all-site VCF, a
.fai, or bcftools-specific annotations.
- Run the subcommand and redirect output into a new file, because most modes write transformed text to stdout.
- 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.
