How to get multiple genes from bam files

Question

[沛煒]

Hello guys, I am working on a pool-seq data with 80 genes sequenced from 400 individuals.

I have aligned them to the reference and got 400 bam files.

I'd like to get all of the 80 genes and write them into 80 fasta files (each contains 400 orthologous sequences).

I already knew the location of each gene on the reference (e.g., gene1 at C1:12211-13100, gene2 at C5: 56733-56823...).

Does anyone have any suggestion to output the fasta files separated with genes?

Thanks