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ERROR MESSAGE: SAM/BAM file 1.dedup.bam is malformed: SAM file doesn't have any read groups defin ed

I use the GenomeAnalysisTK.jar to mark realignment,but get a error message.

EXOME_interval.list :java java -Xmx10048m -jar GenomeAnalysisTK.jar -R ref.fasta -T RealignerTargetCreator -o 1.realn.intervals -I 1.dedup.bam

ERROR MESSAGE: SAM/BAM file 1.dedup.bam is malformed: SAM file doesn't have any read groups defin
ed in the header. The GATK no longer supports SAM files without read groups

Can you please let me know what is the problem in my file.

Thank You in advance.

Answers

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