Creating a BWA index with an index_prefix

Question

[genomics Newbie]

Because of a software requirement the version BWA v0.7.8 is required.

Using https://hcc-docs.unl.edu/display/HCCDOC/Running+BWA+Commands and the following

bwa index [-a bwtsw|is] input_reference.fasta index_prefix

where input_reference.fasta is an input file of the reference genome in fasta format, and index_prefix is the prefix of the generated index files.

I ran the command 'bwa index -a bwtsw /hg19_reference/hg19_exome.fa hg19'

Expected Outcome: BWA index files would have a hg19 prepended (i.e. hg19.amb, etc) and not be created in the same file folder as my reference genome.

Question 1: What is the command that I can use to prepend (I thought this was the index_prefix) hg19 to the index files? Is there a -p before the index_prefix?

Question 2: Where should the index files really be created? In the BWA directory or the genome reference file folder?

Question 3: Which are the index files? hg19_exome.fa.sa, hg19_exome.fa.pac, hg19_exome.fa.fai, hg19_exome.fa.bwt, hg19_exome.fa.ann, hg19_exome.fa.amb, hg19_exome.fa

Answer 1

[GenoMax]

1: If you want to get the hg19 prefix for your index files then run (adjust file paths as needed) bwa index -a bwtsw hg19_reference/hg19_exome.fa -p hg19
2 : They should be created in the directory where you are running this command from
3 : All those files make up the index set

[genomics Newbie]

Thank you. My command only generated the following indexes...hg19.sa, hg19.amb, hg19.ann hg19.bwt and hg19.pac. I did not see any hg19.fa index. Any ideas why the command did not generate the hg19.fa?

[GenoMax]

hg19.fa would have been the original fasta format file which in your case is hg19_exome.fa. You could create a soft link like so ln -s hg19_exome.fa hg19.fa.

Since you specifically wanted the prefix hg19 for your index we added the -p hg19 to the command above. Otherwise you could just run bwa index -a bwtsw hg19_reference/hg19_exome.fa and get the index files that have the prefix of the fasta file name like you posted in original question.

[genomics Newbie]

Thank you for your reply! For this question I didn't see an accept button.

[GenoMax]

I have moved my original comment to an answer. If you found it useful you can accept it.