How To Load A Custom Genome With The Readvcf() Command (Bioconductor)

Question

[Yannick Wurm]

Hello,

Loosely imitating http://www.bioconductor.org/help/workflows/variants/

library(VariantAnnotation)
readVcf("myvcf.gz")

This fails - readVcf requires "genome" argument... which I do not have because I work with a nonmodel organism. So how can I create a custom genome object that makes it possible to load a VCF from a non-model organism into R?

I want to have my Vcf in GRanges format for subsequent plotting with ggbio....

Thanks & kind regards, Yannick

Answer 1

[Yannick Wurm]

Whoops! It turns out that the custom genome doesn't really have to be a genome - any character string will work! Thanks Bioconductor mailing list for the answer

  readVcf("myvcf.gz", "myDogRex")    # no problem!