[BioC] DNAStringSet_translate error in predictCoding()
"Dr. Jörg Linde"
joerg.linde at hki-jena.de
Tue Jun 17 14:45:44 CEST 2014
Dear bioconductor team,
I have a problem with predictCoding() of the VariantAnnotation library
posing an error which is the same as described here:
Howerver, after reading my vcf it clearly has a DNAStringSetList in
it's ALT variable.
The problem remains when using vcftools to remove indels from the vcf.
As far as I see there are some ALTs with two possibilities.
Is there anything else which could cause the problem?
I am also aware of this thread
but I can't figure out how to remove those lines causing the problem.
Thank you very much
coding <- predictCoding(vcf, txdb, seqSource=fa)
Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup,
in 'x[]': not a base at pos 3
DNAStringSetList of length 142721
<142711 more elements>
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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