DoC for genes

= Depth of Coverage per gene = source: gatk_walkers_coverage_DepthOfCoverageWalker

java -Xmx4g -jar GenomeAnalysisTK.jar   \ -R ucsc.hg19.fasta       \ -T DepthOfCoverage   \ -o  $i.depthofcoverage     \ -I   $i.realigned.recal.bam         \ -geneList  refGene.sorted.txt  \ -ct 6 -ct 8 -ct 10 -ct 20  \ -L  exon.target.interval_list \ -omitBaseOutput \ -omitLocusTable