How to calculate kinship matrix table from vcf file

Question

[rj.rezwan]

Hi, I have a variant file subset_filtered.vcf.gz and want to calculate the kinship values from the file. Could anyone please guide me on calculating the kinship matrix to generate the heatmap from this?

Answer 1

[barslmn]

You can use the vcftools relatedness2 module. Which implements the method describes in the paper: https://academic.oup.com/bioinformatics/article/26/22/2867/228512

vcftools --gzvcf subset_filtered.vcf.gz --relatedness2

You can then use multiqc to create the heatmap. -ip produces interactive graphs, -s writes full sample names, -f forces overwrite.

 multiqc -ip -f -s ./

[chrchang523]

The last vcftools release was in 2018. It has been superseded by bcftools for most purposes, and by plink 1.9/2.0 for most analytical functions which didn't get included in bcftools.

In this case,

plink2 --vcf subset_filtered.vcf.gz --make-king-table

is far more efficient than vcftools. I just tested this on a Mac on 10% of 1000 Genomes phase 3 chr21, and it took 1.1 sec using plink2 and more than 22 minutes using vcftools, even though plink2 was forced to waste time converting the VCF to its native file format.