bwa index option bwtsw

[sowmyai]

I am having a hard time understanding the bwtsw option in bwa index command.

1. What does this do that is different from the is option and why is it recommended for longer (>10 MB) reference genomes ?

2. Does it have anything to do with the actual alignment with indels (using Smith-Waterman) ? Or is the "sw" in "bwtsw" just a coincidence ?


3. What is the relation between this and bwasw ? Should I use both or neither ? Or are they completely independent of each other ?

4. Does using this option change the alignment output or is it just a better/faster indexing technique for large reference genomes ?

Sowmya

[sowmyai]

Anyone ? Or maybe reference to someplace I can get the answers from ?

[lh3]

1. -a is uses too much memory
2. indexing is implemented in bwtsw
3. unrelated
4. output is not changed

All you need to know is that bwtsw is the proper option for long genomes. The bwa manual is pretty clear about this.