How to map multiple CDS sequences to exome data using bwa mem? Normally, I use bwa-mem to map my fastq reads for a bunch of species using one protein-coding gene CDS from my reference species. This was fine when I had to try it for just a group of genes...I would obtain single CDS fastq files and use them as a reference.
However, we now want to obtain protein-coding sequences for ALL GENES in my exome datasets. If I have one file containing all the CDS from my reference species, can that be used in bwa-mem? The end of my custom script produces one multiple sequence alignment file when I ran it using one gene only...my concern is that bwa-mem will somehow replace certain CDS or would I just end up with over 20000+ MSAs?  Which is fine because I need them to be individual MSAs for each protein-coding gene.

I use a simple python script at the end to extract base information from the mpileup files generated to create my MSAs.
If I have one file containing all the CDS from my reference species, can that be used in bwa-mem? 


That's fine, normal usage of bwa-mem entails giving it a fasta file with all chromosomes/contigs/transcript/etc. in an organism, so your usage is no different. How your custom "make an MSA" script handles that is unknown of course.