I'm using 1000 genomes pilot data, I've downloaded 3 zipped files. And I then use all three in the same command so it looks like this:
bwa index input_1.fastq input_2.fastq input_3.fastq
This produces 5 files, 2 are binary and 3 are fastq again.
But the usage for BWA-mem asks that the index be specified as 1 file, what's going on here? thanks!