Runs bowtie2

Alignment mode selection added, user can choose between local and global
mode
Configuration file

Contains paths to all tools and databases
run picard tools to sort sam files, add read group and fix mate info

User can now enter lane info for the sample
Runs fastqc and sickle

Perform quality based trimming of fastq files
Run indel realignment and base score recalibration
Run exome seq/ dna seq analysis

Now accepts multiple samples
Perform variant detection and annotation

Now uses unified genotyper
Merge pull request #1 from shashidhar22/version2

Version2