[BioC] DNAStringSet_translate error in predictCoding()

[Valerie Obenchain]

Hi Rebecca,

It looks like your ALT variable may contain structural variants. When 
structural variants are present in a vcf file, readVcf() will convert 
this to a CharacterList instead of a DNAStringSetList.  Try,

alt(vcf)

and see if you have a DNAStringSetList. If instead you have a 
CharacterList, see this thread for how you can subset the vcf on 
non-structural variants.

https://stat.ethz.ch/pipermail/bioconductor/2012-October/048370.html

Valerie


On 10/31/12 16:44, sun wrote:
> Hi all,
>
> I got an error when I used predictCoding() in VariantAnnotation package.
>
>> coding<- predictCoding(vcf, txdb, injected_Arabi)
> Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup,
> skipcode,  :
>    in 'x[[24606]]': not a base at pos 3
>
> How can I get the value of x[[24606]]? Any suggestion for the debugging?
>
> Thanks,
>
> Rebecca
>
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