Usually when I use alignment with bwa, I follow this script:  

  <code>bwa aln reference.fa sample.fastq.gz > sample.sai</code>

But this time I have manifest.txt and I want to target specific regions with this and I want to speed the alignment process with specific output. If It is possible in BWA, I would like to get your answers. Any help is much appreciated. 

   Thanks in advance. 
you need to map everything first, convert this "manifest.txt" file as a bed file and extract the regions. https://www.biostars.org/p/49306/