vcftools安装及使用

manual

vcftools documentation

vcftools is a suite of functions for use on genetic variation data in the form of VCF and BCF files. The tools provided will be used mainly to summarize data, run calculations on data, filter out data, and convert data into other useful file formats.

一、安装

conda install -c bioconda vcftools

二、功能概览

常用功能如下，待具体用到时再做详细补充：

Get basic file statistics

Applying a filter

Writing to a new VCF file

Converting a VCF file to BCF

Getting allele frequency

Getting sequencing depth information

Getting linkage disequilibrium statistics

Getting Fst population statistics

Converting VCF files to PLINK format

三、简单使用

1、查看统计信息

$ vcftools --vcf snps.filtered.pass.vcf --counts
#After filtering,kept 1 out of 1 Individuals
#After filtering,kept 12114 out of a possible 12114 Sites

$ vcftools --vcf snps.filtered.pass.vcf --depth -c > depth_summary.txt
$ cat depth_summary.txt
#INDV N_SITES MEAN_DEPTH
#cbp 12114 124.526

2、群体vcf文件过滤

参见SNP Filtering Tutorial

教程写得非常详尽

3、计算allele, depth, LD, pi, fst, TajimaD, SNP density等统计参数

具体使用案例待补充，或可参考manual

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未完待续