package R for vcf file ??

Question

[Picasa]

Hello,

I'm looking for a package in R which can deal with vcf file and doing stuff like "phyloseq" (which deal with .biom file) such as figure, statistics etc.

Do you know some ? thanks

Answer 1

[ivivek_ngs]

You can take a look at this link. There is a package known as VariantAnnotation. You can use this to read the vcf files and then use phyloseq R package. Hope this helps!

Answer 2

[Mo]

This can help you with a workflow

source("http://bioconductor.org/workflows.R"")
workflowInstall("variants")

You can have a look at here for more info like tutorial etc

If you want to extract your data , you can check this one here which is very well explained so I don't write what is written before

You can also check what people have said already on Biostar (look at the right side of your question) for example this is roughly answering your question