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Old 07-13-2010, 10:19 AM   #5
Location: Ithaca, NY

Join Date: Apr 2010
Posts: 39

That would most likely be the issue! You need to combine the chromosomes into one file. On a *nix machine, say each is named chr##.fa (I know it's this way for the horse.. chr1, chr2, chr3, ... chrX) - you would do
cat chr*.fa > genome.fa
This tells it to put the contents of all files in the new file genome.fa. Then you index, but, you probably want to use -a bwtsw.. I believe not including that flag was my error. So, you'd do
bwa index -p prefix -a bwtsw genome.fa
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