Hi Jennifer,
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
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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().
Valerie
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: jb...@illumina.com <mailto:jb...@illumina.com>
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