how to use ExtractSubsetOfBAMBasedOnBedFile with SVAs, ALUs....bed files

[alerubio]

Hello.
Is it possible to use 'ExtractSubsetOfBAMBasedOnBedFile' to extract reads aligned to SVA or ALU sites using the corresponding bed files?
it seems that this script only works for L1HS its output is called 'sample....L1HsOnlly.fastq'

#!/bin/bash

This script launches runExtractSubsetOfBAMBasedOnBedFile.sh for every pair of bam and region files

Usage: runExtractSubsetOfBAMBasedOnBedFileShell.sh path-bam path_reg thresh-mismatch(3)