Dear All, I need to setup BWA for alignment. I followed below steps:

1-downlod reference genome version through 'wget' and below link:

Wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

2-then extract the downloaded file:

tar zvfx chromFa.tar.gz

3- 'cat' .fa file to wg.fa :

cat *.fa > wg.fa

4- remove additional files:

rm chr*.fa

5- Now, I have to generate an index file through the below command by bwa version 0.7.17-r1188:

./bwa index -p hg19bwaidx -a bwtsw wg.fa

After that in the folder I have these 5 files:
hg19bwaidx.amb, hg19bwaidx.ann, hg19bwaidx.bwt, hg19bwaidx.pac,hg19bwaidx.sa

6- Now, I would like to generate a SAM file for a paired-end through mem algorithm based on the below command:

./bwa mem  -T 19  ?????  file_paired_1.fastq  file_paired_2.fastq  > aln.sam

My question is that which one of the five files generated in the indexing process(step 5) should I use instead of ????? at step 6?

I appreciate it if anybody shares his/her comment with me.

Best Regards,