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bwa mem -R option

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  • bwa mem -R option

    Trying to use bwa mem with the -R option to add read group headers to the alignment output in one step, but it keeps coming back with the error:

    [E::bwa_set_rg] no ID at the read group line

    Below was what I tried for paired-end reads and then for all single reads:

    bwa mem -aM -R @RG\tID:Seq01p\tSM:Seq01\tPL:ILLUMINA\tPI:330 Refgen Seq01pair1.fastq Seq01pair2.fastq > Seq01pairs.sam

    bwa mem -aM -R @RG\tID:Seq01a\tSM:Seq01\tPL:ILLUMINA\tPI:330 Refgen Seq01all.fastq > Seq01all.sam

    If I take out the entire -R option, bwa mem appears to run just fine. I suppose I can always add the read group header on later with Picard or samtools, but it would be nice to add it now....

    Wondering if there is something wrong with my read group ID line? Has anyone else successfully run bwa mem with the -R option and what did you use?

  • #2
    I"m not sure but try quotes for your mem argument ...

    bwa mem -aM -R "@RG\tID:Seq01p\tSM:Seq01\tPL:ILLUMINA\tPI:330" Refgen Seq01pair1.fastq Seq01pair2.fastq > Seq01pairs.sam

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    • #3
      Thanks for the quick (and correct!) response - I tried it with the quotes, and it worked!

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