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