[BioC] VariantAnnotation: readVcf on nonmodel organism

Valerie Obenchain vobencha at fhcrc.org
Wed Sep 26 20:49:41 CEST 2012

Hi Yannick,

The 'genome' argument to readVcf() is a character string specifying the 
build of the genome the variants are mapped to. It's present use is for 
your own bookkeeping so there are no "invalid" strings. In this case 
using the build that is on NCBI would be logical or you could use your 
own tag,

readVcf("mymappings.vcf.gz", "draftgenome")


On 09/26/2012 10:56 AM, Yannick Wurm wrote:
> 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
> --------------------------------------
> 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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