How To Load A Custom Genome With The Readvcf() Command (Bioconductor)
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11.6 years ago
Yannick Wurm ★ 2.5k

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

vcf r • 2.9k views
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Entering edit mode
11.6 years ago
Yannick Wurm ★ 2.5k

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!
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