[Bioc-devel] VariantAnnotation: Same locus, multiple samples

[Michael Lawrence]

I don't see how this can be fixed. The two data structures are semantically
incompatible; they encode different types of information, so information is
lost in both directions. Even if we collapsed the alts, there is no way (as
far as I know) to say that data for one individual + alt combination is
absent. We could put NA (".") for every value concerning that alt, but it
seems too big of an assumption to say that all(is.na())) implies omission
of the VRanges element. In other words, VCF is rectangular and VRanges is
ragged, and there is no established way to encode the raggedness in the VCF.



On Mon, Dec 8, 2014 at 11:27 AM, Valerie Obenchain <vobencha at fredhutch.org>
wrote:

> This could be fixed in the VRanges -> VCF coercion or in VCF -> VRanges.
>
> Currently VRanges -> VCF creates a VCF with >1 row per position (ie, does
> not collapse ALT values). I'm not sure this is technically valid as per the
> specs, however, it may have been by design to meet another need. If we are
> ok with >1 row per position the change can be made in VCF -> VRanges.
>
> Opinions?
>
> Valerie
>
>
>
> On 12/05/2014 01:18 AM, Julian Gehring wrote:
>
>> Hi,
>>
>> Assume that we have two variants from two samples at the same locus,
>> stored in a 'VRanges' or 'VCF' object:
>>
>>    library(VariantAnnotation)
>>
>>    vr = VRanges("1", IRanges(c(10, 10), width = 1),
>>      ref = c("C", "C"), alt = c("A", "G"),
>>      sampleNames = c("S1", "S2"))
>>    vcf = as(vr, "VCF")
>>
>> If we convert the VCF to a VRanges, we now get each variant in each
>> patient:
>>
>>    vr2 = as(vcf, "VRanges")
>>
>>    length(vr) ## 2
>>    length(vr2) ## 4
>>
>> It seems that the VCF object does not store the information of the
>> 'sampleNames' in the first conversion.
>>
>> Best wishes
>> Julian
>>
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>>
>>
>

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