Variant calling based on RNA-Seq

RNA-Seq variant calling pipeline according to GATK Best practices.

Run mRNA-Seq variant pipeline

bash mRNA.variant_master.sh -d {raw_directory}

arguments:
d=[d]irectory with raw data (directory; required)  
g=directory with the reference [g]enome  
    accepted values: GRCh98, Mmul_8  
e=[e]mail address