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Hi, I'm currently working with bwa, samtools and GATK to make SNP calling on Medicago truncatula. I'm using my own reference sequence, with the 8 chromosoms in the same fasta file.

C1_lenght=155648 AAAGATAGAGA.. C2_lenght=125018 ATGGATC... etc.. I have done alignments without problem, but for GATK : I do rmdup --> CreateSequenceDictionary.jar (picard) --> samtools sort --> Read Group (picard) --> samtools index and then : Pre alignment with :

java -jar -Xmx4g /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -nt 8 -T RealignerTargetCreator -R REF.fa -o RTC.intervals -I INPUT_muq30_RMDUP_RG.bam

Here there is no problem, but when I want to make the realignement :

java -jar -Xmx4g /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -T IndelRealigner -R REF.fa -I INPUT_muq30_RMDUP_RG.bam -targetIntervals RTC.intervals -o INPUT_muq30_RMDUP_RG_REAL.bam

And I got this error message : ERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the provided reference: '13'

I didn't find any explanation in google for this error. Could you please help me ?!

vschilling