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

[Valerie Obenchain]

Michael,

This is implemented in 1.7.48. AD is expanded as a list matrix where 
each list element holds a REF,ALT pair.

Val


On 09/05/2013 07:36 AM, Valerie Obenchain wrote:
> Hi,
>
> 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.
>
> Thanks.
>
>>
>> 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.
>
> Val
>
>>
>> Michael
>>
>>     [[alternative HTML version deleted]]
>>
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