7c7 < /usr/bin/java -jar /usr/local/share/GenomeAnalysisTK.jar -T IndelRealigner -R ${h37}sami.fasta -I ${dir}processed/${bamfile}.bam -targetIntervals ${dir}processed/${bamfile}.bam.intervals -o ${dir}processed/${bamfile}_realigned.bam # step2 --- > /usr/bin/java -jar /usr/local/share/GenomeAnalysisTK.jar -T IndelRealigner -R ${h37}sami.fasta -I ${dir}processed/${bamfile}.bam -targetIntervals ${dir}processed/${bamfile}.bam.intervals -o ${dir}processed/${bamfile}_realigned.bam --defaultBaseQualities 12 # step2