ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '1
Hi GATK team
When trying to run GATK with the following command, I encountered an error.
this is the command:
java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R YBT1518_ref.fa -A SnpEff -V 1YBT1518-sp1-1.vcf --snpEffFile 1YBT1518-sp1-1.vcf.ann -L 1YBT1518-sp1-1.vcf -o 1YBT1518-sp1-1.final.vcf
And the error is: ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '13'
I wonder whether there is a problem with my reference, but I prepare my reference as is said on this page http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference.
Thanks a lot for your advice in advance