#!/usr/bin/perl -w
use strict;
use File::Temp qw(tempfile);
# Usage perl 1by1.pl for SATSUMA analysis
# User need to set the reference multifasta file name her...
...on
--gatk-config-file PATH/TO/GATK/PROPERTIES/FILE
gatk forwards commands to GATK and adds some sugar for submitting spark jobs
--spark-runner cont...