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  • FGponce
    Junior Member
    • Dec 2011
    • 9
    #1

    Trouble with RG line

    Hi,
    am trying to add RG line to a Sam made after bwa alignment prior to GATK.

    This is the command:
    bwa sampe -f OD.sam -r "@RG\tID:<ODexome>\tLB:<ODexome>\tSM:<ODexome>\tPL:ILLUMINA" hg19 OD_R1.sai OD_R2.sai SampleR1_001.fastq SampleR2_001.fastq

    BUT get this error!

    [bwa_sai2sam_pe] malformated @RG line

    Any ideas?

    Cheers,

    FGP
    Last edited by FGponce; 01-31-2013, 10:41 PM.
    Tags: None
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