Tagged with #genomeanalysistk.jar
0 documentation articles | 0 announcements | 1 forum discussion

No posts found with the requested search criteria.
No posts found with the requested search criteria.
Comments (14)

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 ?!