Burrows Wheeler Aligner - tool

Question

[sruthi]

Hi, I'm new to BWA tool. I indexed my reference.fa using command:

bwa index -a bwtsw reference.fa reference_prefix

and got 3 output files: .amb .ann .pac

I read that the above command must produce 8 output files such as .amb .ann .bwt .pac .rbwt .rpac .rsa .sa.

As only 3 output files have been generated, has the command run successfully? If not what should I do?

TIA

[h.mon]

bwa index output some messages to the screen, what did they say?

[sruthi]

Hey, So the messages displayed are: 1. bwa_index Pack FASTA 2. Construct BWT for the packed sequence 3. BWT_gen 4. Update BWT 5. Pack forward only FASTA 6. Construct SA from BWT and Occ...

[lakhujanivijay]

What is the reason that you chose bwtsw ?

[sruthi]

Hey, I chose bwtsw as the genome I'm analysing is of larger size, say 3.3 GB. Hence.

Answer 1

[Joe]

That command produces 5 files for me: .amb, .ann, .bwt, .pac and .sa.

bwa Version: 0.7.17-r1188

[sruthi]

Hey healey, I ran the command for the second time and got all these 5 files as the output. Thanks.