[BioC] VariantAnnotation: readVcf on nonmodel organism
y.wurm at qmul.ac.uk
Wed Sep 26 19:56:21 CEST 2012
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).
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
More information about the Bioconductor