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  • bwa index from reference with unusual chromosomes

    A similar question to http://seqanswers.com/forums/showthread.php?t=8951

    I'm about to create my reference index for aligning some exome data. I wonder should I includes these chromosomes in the reference index. At first I thought "what could be the harm" but I will be using GATK downstream, and GATK doesn't work if the chromosomes are out of order. How then should I handle these non-canonical chromosomes when there is no implicit order.

    Thanks for any advice

  • #2
    Use the 1000 genomes reference, and you should have no problems..

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