[BioC] VariantAnnotation: readVcf on nonmodel organism

Yannick Wurm y.wurm at qmul.ac.uk
Wed Sep 26 19:56:21 CEST 2012

Dear list,

I work with a non-model organism (an ant) for which we sequenced the genome. The genome is on NCBI but isn't annotated in the standard R-accessible databases. 

I'm now trying to load a VCF file into R (with the aim of subsequent plotting with ggbio). 

> library(VariantAnnotation)
> readVcf("mymappings.vcf.gz")

This fails because readVcf wants a "genome" argument. I haven't been able to find an example using a non-established genome. How can I generate such a genome for my species? The genome is in the form of 10,000 scaffolds. I'm looking for a quick hack, not a complex submission to another database. 

FWIW This is on R 2.15.0 with latest bioconductor.

Thanks for your help & kind regards,


Yannick Wurm http://yannick.poulet.org
Ants, Genomes & Evolution ⋅ y.wurm at qmul.ac.uk ⋅ skype:yannickwurm ⋅ +44 207 882 3049
5.03A Fogg ⋅ School of Biological & Chemical Sciences ⋅ Queen Mary, University of London ⋅ Mile End Road ⋅ E1 4NS London ⋅ UK
Easy custom BLAST interface: http://www.sequenceserver.com

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