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