Post date: Aug 27, 2014 5:19:31 PM
First identify intervals to realign,
cd /home/A01963476/data/timema/moe_radiation_wgrs/alignments/
java -Xmx8g -jar /rc/tools/free/redhat_6_x86_64/gatk-3.1.1/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /labs/evolution/data/timema/draft_genome/draft0.3/mod_lg_timemaGenome.fasta -I aln_WTCHG_135840_296_unique.bam -o aln_WTCHG_135840_296_unique.intervals