[Bioc-devel] VariantAnnotation writeVcf problem

Valerie Obenchain vobencha at fhcrc.org
Wed Nov 20 18:27:41 CET 2013

Hi Jennifer,

I've cc'd your message to the Bioconductor mailing list. We have two 
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writeVcf() should only write out '.' for ID if the ID is missing. There 
is no restriction on the format of the ID. Can you provide a small 
sample of the vcf file you're having trouble with (just a few lines is 
enough)? Also include the output of your sessionInfo().


On 11/15/2013 08:56 AM, Becq, Jennifer wrote:
> Hi Valerie,
> I’ve been using VariantAnnotation for quite a while now and it’s been great!
> However I’ve just encountered a problem:
> If I read in a VCF and re-write it directly, the ID column has
> disappeared and becomes “.” instead of the original
> “DEL:9586:0:1:0:0:0”, even though the rownames of my VCF object are
> correctly populated with the original ID column.
>  > library(VariantAnnotation)
>  > in1 = readVcf("my.vcf.gz", "hg19")
>  > writeVcf(in1, "test.vcf")
> I was wondering if that was because ID only accepts a specific format
> (rsID or chr:pos)?
> Thank you for your help
> Jennifer
> *Jennifer Becq*
> *Bioinformatics Scientist*
> *Illumina Cambridge Ltd*
> Tel: +44 (0) 1799 532300
> email: jbecq at illumina.com <mailto:jbecq at illumina.com>

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