[Bioc-devel] VariantAnnotation: VCF to VRanges with multiple INFO values

[Valerie Obenchain]

Thanks to Michael and Julian for taking care of this. Fixes are in 
devel, >= 1.13.15.

Valerie


On 12/03/14 08:44, Michael Lawrence wrote:
> Looks like an issue when expand()ing the VCF. Maybe Val could take a look?
>
> On Wed, Dec 3, 2014 at 7:39 AM, Julian Gehring <julian.gehring at embl.de>
> wrote:
>
>> Hi,
>>
>> The conversion from a 'VCF' to 'VRanges' object fails if an INFO field
>> with multiple values for different ALT alleles is present:
>>
>> Here an example VCF entry for which this fails (line 71151250 in
>> 'ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz'
>> , taken from
>>
>> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz
>> ):
>>
>>    10001541      rs12451372      C       G,T     100     PASS
>>
>> AC=700,298;AF=0.139776,0.0595048;AN=5008;NS=2504;DP=17289;EAS_AF=0.2421,0;AMR_AF=0.1801,0.0115;AFR_AF=0.0749,0.2194;EUR_AF=0.0915,0;SAS_AF=0.1431,0;AA=T|||
>>
>> The respective code to reproduce this:
>>
>>    library(VariantAnnotation)
>>    roi = GRanges("17", IRanges(1e7+1541, width = 1))
>>    vcf = readVcf(path, "GRCh37", ScanVcfParam(which = roi, info = "AF"))
>>    ## 'info = character()' and other versions also cause the error
>>
>>    vrc = as(vcf, "VRanges") ## error
>>
>> fails with
>>
>>    Error in colSums(ielt) : 'x' must be an array of at least two dimensions
>>
>> This occurs both with the latest version of VariantAnnotation in
>> bioc-release and bioc-devel.
>>
>> Best
>> Julian
>>
>> _______________________________________________
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>>
>
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