Hi, I regularly use "NGS: SAM Tools/Filter SAM" tool. Filtering after mapping with BWA is a required step. I feel my current approach to reintroduce the header after filtering is very wasteful. Wouldn't be great if this tool had an option to keep the header? This sounds simple enough. In fact looking at the logic in the python script: for line in infile: line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ) and not line.startswith( '@' ) : fields = line.split( '\t' ) flags = int( fields[flag_col] ) valid_line = True for index, opt_bool in used_indices: if bool(flags & 0x0001 << index) != opt_bool: valid_line = False break if valid_line: print line It seems like it could be done by adding at most a couple of lines. Also, most of the time after filtering what you really want is a sorted BAM file. Most tools dealing with SAM/BAM files in Galaxy already have the option to output a sorted BAM file. I think it would be nice if "Filter SAM" followed the same path. Are these enhances in the radar? Would you take a pull request implementing them? Best, Carlos