bwa index from reference with unusual chromosomes

[DavyK]

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

[nilshomer]

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