cygwin_bash_path = 'D:/Cygwin/bin/bash.exe'
from subprocess import check_call, CalledProcessError
arguments = [cygwin_bash_path, bedtools_exe_path, 'intersect', '-a', gene_bed_file, '-b',
             snp_bed_file, '-wa', '-wb']

with open(output_file,"w") as f:
    try:
        check_call(arguments,stdout=f)
    except CalledProcessError as e:
        print(e.returncode)