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  • missing read groups for unaligned reads

    Hi everyone,

    I am using bwa to align Illumina reads. I used the -r option in order to specify the read group.
    In the output sam file I am getting read groups only for the aligned reads. Reads that are not mapped (with '*' in the chromosome and position) don't have a read group.
    In the downstream analysis I use GATK, which gives errors because of this.

    Any suggestions how to overcome this?

    Thanks

  • #2
    I have the same problem, I also use bwa -r for alignment.

    When I re-run TableRecalibrate with the added parameter

    --default_read_group name_of_my_read_group

    it seems to work and ignores the unmapped reads. However, I'm not sure this will cause any trouble in downstream analysis?

    Comment


    • #3
      you should join the bwa mailing list. already fixed a while ago.

      Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) - lh3/bwa

      Comment

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