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

[Valerie Obenchain]

Now in IRanges 2.0.1 and VariantAnnotation 1.12.7.

Valerie


On 12/11/2014 09:32 AM, Julian Gehring wrote:
> Can you backport the fixes to bioc-release which is also affected?
>
> Best
> Julian
>
>
> Valerie Obenchain (12/09/14 03:24):
>
>> 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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
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>>>
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