[Bioc-devel] Question for VariantAnnotation package for type G field

[Valerie Obenchain]

Hi Katsuhito,

I've cc'd your message to the Bioconductor mailing list. We have two 
lists, one for general questions and the other for bug reports/feature 
requests. Please post future questions to one of these lists instead of 
sending them to a single person. The lists reach a wider audience and 
others can chime in with their responses/experience. You can find info 
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This bug was fixed in the devel version a few weeks ago. I've pushed the 
fix to release, version 1.8.6, which will be available via biocLite() 
tomorrow ~10am PST.

Valerie

On 11/20/2013 01:05 PM, Yasuno, Katsuhito wrote:
> Dear Valerie,
>
> When I read VCF files, I realized that elements of PL field (Number = G)
> always have
> extra slots with NA. In fact, when writing the corresponding vcf object
> to a VCF file, it causes
> NA's to be printed. Can your package handle Number = G fields? Thanks
>
>                  ID10-1    ID100-1   ID100-35  ID100-36  ID101-1
> 21:9908330_A/G  Integer,4 Integer,4 Integer,4 Integer,4 Integer,4 <- 1
> alternate allele
> 21:9908348_C/T  Integer,4 Integer,4 Integer,4 Integer,4 Integer,4
> 21:9908370_G/A  Integer,4 Integer,4 Integer,4 Integer,4 Integer,4
> 21:9909124_C/T  Integer,4 Integer,4 Integer,4 Integer,4 Integer,4
> 21:10862573_T/C Integer,4 Integer,4 Integer,4 Integer,4 Integer,4
> 21:10862598_C/A Integer,9 Integer,9 Integer,9 Integer,9 Integer,9 <- 2
> alternate alleles
>
>  > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
> [1] VariantAnnotation_1.8.5 Rsamtools_1.14.1
> Biostrings_2.30.1       GenomicRanges_1.14.3    XVector_0.2.0
> [6] IRanges_1.20.5          BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.24.0   BSgenome_1.30.0
> Biobase_2.22.0         DBI_0.2-7              GenomicFeatures_1.14.2
>   [6] RCurl_1.95-4.1         RSQLite_0.11.4
> XML_3.98-1.1           biomaRt_2.18.0         bitops_1.0-6
> [11] rtracklayer_1.22.0     stats4_3.0.2
> tools_3.0.2            zlibbioc_1.8.0
>
> Best,
> Katsuhito
>
> ############################
> Katsuhito Yasuno, PhD
> Department of Neurosurgery
> Yale University School of Medicine
> 1 Gilbert Street, TAC S327
> New Haven, CT 06510
> katsuhito.yasuno at yale.edu
> (203) 785 3056
> ############################
>
>