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
about the mailing lists here,
http://www.bioconductor.org/help/mailing-list/
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.yas...@yale.edu
(203) 785 3056
############################
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