Merge pull request #135 from Gerbenvandervries/master

loading R/2.14.2 version for GATK/1.2-1-g33967a4 UnifiedGenotyper
changed protocols, edited parameter tmpvariables to tmpfolders/files created by a function in the header
removed unused tmp folders
removed fi
Merge pull request #136 from RoanKanninga/master

changed protocols, edited parameter tmpvariables to tmpfolders/files cre...
changed a parameter
Merge pull request #137 from RoanKanninga/master

changed a parameter
new Chromosome merge, and variantspit protocol