[Bioc-devel] expand,VCF and the AD geno field

Valerie Obenchain vobencha at fhcrc.org
Thu Sep 5 16:36:40 CEST 2013


On 09/04/2013 04:23 PM, Michael Lawrence wrote:
> Hi, Val,
> I just fixed expand,VCF to support multiple 'A' columns in info. Looks like
> expand,DataFrame does a cartesian product of list columns, which is not
> what we want in that case.


> Ran up against another hurdle though: the conventional AD genotype field
> has a (virtual) Number of 'A+1', but since VCF does not have such a thing,
> it's Number is typically missing. Should we special case this one and have
> it keep yield a ref,alt pair for each alt? Opinions?

At the moment I can't think of a better option. Looking around the 1000 
Genomes page I didn't find other fields that had this 'ref + alt' 
length. So, implementing an option for the user to specify a field name 
and expansion type ... etc. seems like overkill.

I'm fine with special casing it until more fields of this type come up.


> Michael
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list