How to use R language to calculate nucleotide diversity using vcf format file

This article is about how to use R language to use vcf format files to calculate nucleotide diversity. I think it is very practical, so I share it with you. I hope you can get something after reading this article. Let's take a look at it.

The first is to use bcftools software to manipulate the vcf file to split the vcf file according to the chromosome bcftools view snp.vcf.gz scaffold_1 > popgenome-vcf/scaffold_1

Bcftools view snp.vcf.gz scaffold_2 > popgenome-vcf/scaffold_2

If there are only vcf files in the current directory, you will encounter an error Failed to open .vcf.gz: could not load index. Please refer to https://www.cnblogs.com/chenwenyan/p/11945445.html.

Tabix-p vcf snp.vcf.gz

If there is no popgenome-vcf in the current directory, you also need to create a new directory.

Mkdir popgenome-vcf

Today's reference article says In theory, the r PopGenome can readVCF files directly, using the readVCF function. However, because our samples are haploid, we need to use a different function, r readData, which requires a folder with a separate VCF for each scaffold. Why is this?

The next step is to read in the data # install.packages ("PopGenome") in R language.

Library (PopGenome)

Getwd ()

Setwd ("VCF/")

Snp