[Bioc-devel] expand,VCF and the AD geno field
vobencha at fhcrc.org
Tue Sep 24 21:16:08 CEST 2013
This is implemented in 1.7.48. AD is expanded as a list matrix where
each list element holds a REF,ALT pair.
On 09/05/2013 07:36 AM, Valerie Obenchain wrote:
> 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
>> 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
>> it's Number is typically missing. Should we special case this one and
>> 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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