Off topic:How to run BBMap and VCFtools for a 200 of WGS .fasta files in a for loop in Shell or Bash without printing file names??

Question

[elvissober]

How to run BBMap and VCFtools for a 200 of WGS .fasta files in a for loop in Shell or Bash without printing file names??

Have been advised to use that code for BBMap:

bbmap.sh ref=ref.fa
(wait for that to finish)
bbmap.sh in=reads1.fq out=mapped1.sam
bbmap.sh in=reads2.fq out=mapped2.sam
bbmap.sh in=reads3.fq out=mapped3.sam

This can`t be used for an automatic pipeline, cause requires file name writing. How to make that using for loop and without need to rewrite file`s names? Thanks.