AssotesteR genotype format

Question

[Quak]

I found AssotesteR package quite interesting to use. However, the genotype file format it works with is different from common format.

as its described, its a numeric matrix or data frame with genotype data coded as 0, 1, 2. and Missing data is allowed.

1. So, basically, I can write a python script to make a table out of a given VCF file. I was curious if someone has already used this package or made such thing.
2. Is there any other library/packages that you can introduce me? preferably with a use-friendly manual!

Answer 1

[zx8754]

We can use VariantAnnotation package to read vcf into R:

myVCF <- readVcf("/path/to/VCF/myvcf.vcf",genome="hg19")

Then we can get genotype using:

 myVCF@assays$data$GT