Use when working with VCF file utilities from the bcftools bioconda package.
vcfutils.pl <command> [arguments]/home/vimalinx/miniforge3/envs/bio/bin/vcfutils.plbcftools toolchain.AC/AN counts in VCF records.varFilter.vcf2fq.# 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
vcfutils.pl is a command multiplexer rather than a single-purpose tool..fai, or bcftools-specific annotations.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.