Updated 5GPM pipeline

1. Updated in-house_parameters_5gpm.csv for new BED file and derived interval files. 
2. Updated 3 protocols to use the standard Targets + 20bp flanking sequence BED file instead of an additional one with 100 bp flanking sequence. 
3. Removed comment lines with SVN keywords from all protocols as we switched to Git.
4. Deleted 3 outdated parameter.csv files that are no longer used.