SKAT with VCF files

[Andréanne Morin]

Hello,

my data is in VCF. However, it seems like I need plink format to be able to get genotype matrix as well as defining SNP sets... is there a way I can use VCF file and be able to define the collapsing region?

Thanks

Andreanne

[Seunggeun (Shawn) Lee]

Hi Andreanne,

There is a R package "SeqMiner" (http://zhanxw.com/vcf2geno/) that can be used to read VCF file. I used it several times, and it works very well.

Thanks,

Shawn

[freeseek]

You can also use plink2 (https://www.cog-genomics.org/plink2/) to convert your VCF file to a plink format you can load with SKAT. The conversion is really fast.