Indexing genomes for bwa

general

bwa index [options] <reference_in>

e.g. bwa index -a bwtsw build37_chr21.fa
-a option defines the algorythm: bwtsw is for long genomes (>2GB)

Usage: bwa index [-a bwtsw|div|is] [-c] <in.fasta>

Options: -a STR BWT construction algorithm: bwtsw or is [is]

        -p STR    prefix of the index [same as fasta name]
        -c        build color-space index

Warning: `-a bwtsw' does not work for short genomes, while `-a is' and

        `-a div' do not work not for long genomes. Please choose `-a'
        according to the length of the genome.