Is your alt allele a DNAStringSetList or CharacterList? I am curious because predictCoding() should have thrown a warning along the lines of 'alt(query) must be a DNAStringSetList' if you had a CharacterList. Otherwise this may be a bug. Can you provide a small reproducible example? Valerie On 10/31/12 21:08, Valerie Obenchain wrote: > 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 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor