21 months ago by
Republic of Ireland
The options for
bwa index are :
Usage: bwa index [options] <in.fasta>
Options: -a STR BWT construction algorithm: bwtsw, is or rb2 [auto]
-p STR prefix of the index [same as fasta name]
-b INT block size for the bwtsw algorithm (effective with -a bwtsw) 
-6 index files named as <in.fasta>.64.* instead of <in.fasta>.*
The standard option for human and mouse would be
-a bwtsw, which creates indices based on the Burrows-Wheeler Transform (BWT).
Thus, to index your FASTA genome, you just need to do:
bwa-0.7.17/bwa index -a bwtsw mm10/mm10.fasta
[bwa_index] Pack FASTA... 52.54 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5461743548, availableWord=396308404
[BWTIncConstructFromPacked] 10 iterations done. 99999996 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999996 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999996 characters processed.