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
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!
This can help you with a workflow
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
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