[BioC] DNAStringSet_translate error in predictCoding()

Valerie Obenchain vobencha at fhcrc.org
Thu Nov 1 05:08:06 CET 2012

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,


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.



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
> 	[[alternative HTML version deleted]]
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