***'all\_samples'** = a list of all BAM files, one /path/2/sample.bam per line (avoid duplicates!)
***'ref_db'** = the reference database in fasta format (f.i. multi-sequence fasta)
***'gen\_pos'** = a list with start and end positions for each sequence (format: sequence_id<tab>start<tab>end<\n>)
***'gen\_pos'** = a list with start and end positions for each sequence (format: sequence_id start end)
***TODO! Format 'db\_ann'** = [optional] a gene annotation file for the reference in [general feature format](http://www.ensembl.org/info/website/upload/gff.html)(GFF).
