vcftools 命令

常用示例

说明

VCFtools is a suite of utilities for analyzing Variant Call Format (VCF) and Binary Call Format (BCF) files, the standard formats for storing genomic sequence variations. It provides comprehensive tools for filtering, manipulating, and computing statistics from variant data. The tool supports filtering variants by quality scores, allele frequencies, missing data, genomic regions, and individual samples. It calculates population genetics statistics including allele frequencies, nucleotide diversity, Fst, linkage disequilibrium, and relatedness measures. VCFtools can convert between formats, compare VCF files, and extract subsets of data for downstream analysis. Output files use the prefix specified by --out with appropriate extensions for each analysis type.

参数

--vcf _file_

Input VCF file (v4.0, v4.1, or v4.2).

--gzvcf _file_

Input compressed (gzipped) VCF file.

--bcf _file_

Input BCF2 format file.

--out _prefix_

Output file prefix. Results are written to prefix.extension.

--recode

Output a new VCF file after applying filters.

--recode-INFO-all

Retain all INFO fields in recoded output.

--chr _name_

Process only variants on specified chromosome.

--keep _file_

Retain only individuals listed in file (one ID per line).

--remove _file_

Remove individuals listed in file.

--maf _float_

Filter by minimum minor allele frequency.

--minQ _int_

Minimum variant quality score.

--freq

Calculate allele frequencies.

--depth

Calculate mean depth per individual.

--relatedness

Calculate pairwise relatedness statistics.

--hap-r2

Calculate linkage disequilibrium statistics using phased haplotypes.