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

[Julian Gehring]

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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