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  • Problem in using GATK to do the realignment

    Hi, I am new to GATK. I met a problem when I tried to use "RealignerTargetCreator" to realign my BAM file. I got error " MESSAGE: SAM/BAM file SC-NL-001_CAGATC_rmdup_reorder.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups".

    According to the answer of http://gatkforums.broadinstitute.org...med-bam-header, it seems the best way to solve this problem is going back to the raw data and do the processing again. I am wondering does it matter which software I am using to do the processing steps before GATK?

    My raw data files are paired-end illumina data. I used "trimmomatic" to get trimmed data. Then I used bowtie 2 to do the alignment.(GATK suggests to use BMA). After that I used samtools to do the sorting and removing the duplicates.(GATK suggests to use Picard) Then I met this problem when I tried to use GATK to do the realignment. Is it because I didn't use the software GATK suggested?

    By the way, how can I get a known indels file of HG19?

    Thank you.

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