The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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