index reference BWA

Question

[manubiomed20]

Can someone help me with the index of reference using BWA?

First, I am not understanding anything of the command quoted by the tutorial that is indicated for index: bwa index [-p prefix] [-a algoType] <in.db.fasta>

I do not understand what exit database prefix means or what it means -a. I've read the manual and I'm not clear.

Another thing I do not understand is how I will select the reference sequence to index. Help-me

Answer 1

[Kevin Blighe]

The options for bwa index are :

bwa-0.7.17/bwa index

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) [10000000]
         -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.
... ...