Update installation.rst

add --data to dbnsfp download
Merge pull request #455 from tanglingfung/patch-3

Update installation.rst
Merge pull request #456 from mjafin/master

Mutect: default to Scalpel instead of SID. Scalpel: use less stringent s...
Ensure joint recalling preparation directories shared when run on muiltiple machines
Copy instead of move the genome/GTF files during genome preparation.
Filter out additional offending reads with problem bases to avoid downstream GATK errors. Handles Ion Torrent input data. Fixes #460
shutils -> shutil. Thanks to Piet Jones.