[Bioc-devel] Bioc 2013 Conference in Seattle, July 18-19 -- Updates

2013-04-25 Thread Martin Morgan
Bioconductors, The Bioc 2013 conference is taking shape with additional sponsors, speakers, and activities. The conference web site is at https://secure.bioconductor.org/BioC2013/ One change is a revised deadline for travel scholarships, now June 10. See you in Seattle! Martin -- Computat

Re: [Bioc-devel] Fwd: [BioC] Problem reading VCF file using readVcf from package VariantAnnotation

2013-04-25 Thread Valerie Obenchain
Hi Vince, Kasper, cc'ing Herve and Marc. I think we have a couple of things going on so I wanted to clarify. The 'genome' argument to readVcf() is assigned to the GRanges in rowData with the "genome<-" setter. This is where .normargGenome() gets called. setReplaceMethod("genome", "Seqinfo",

Re: [Bioc-devel] Fwd: [BioC] Problem reading VCF file using readVcf from package VariantAnnotation

2013-04-25 Thread Kasper Daniel Hansen
An "official" comment on this http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19 with some more info in this discussion https://groups.google.com/a/soe.ucsc.edu/forum/?fromgroups=#!topic/genome/hFp-dGG9gBs Essentially it seems the b37 has been "patched" and this patched release is not reflected i

Re: [Bioc-devel] Fwd: [BioC] Problem reading VCF file using readVcf from package VariantAnnotation

2013-04-25 Thread Kasper Daniel Hansen
I agree with Vincent. I have seen code from Herve in a package with some standardization of chromosome names, and this code could perhaps be used more widely so we don't have all the problems with chr1 vs chr01 vs 1. However, in this particular case, if Ulrich is actually interested in the mitoch

[Bioc-devel] Fwd: [BioC] Problem reading VCF file using readVcf from package VariantAnnotation

2013-04-25 Thread Vincent Carey
I am falling behind. I wanted to have a prototype of the following but I won't do it for a while. We need to make it more convenient to get the right seqinfo metadata in place for a wide variety of artifacts. i propose that there has to be a softer landing for unmet expectations, and some "intel