Realignment

= Realignment = Run the realigner over the intervals to create a cleaned version of the BAM file. Make a temp directory mkdir -p ${tmp_folder}_realign

GATK realignment java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_realign \ -jar $gatk \ -I $PWDS/${subjectID}.mq.srt.bam \ -R $REF \ -T IndelRealigner \ -targetIntervals $PWDS/${subjectID}.forRealign.intervals \ --out $PWDS/${subjectID}.realigned.bam \ -known $DBSNP \ -LOD 0.4 \ -compress 5 \ -l INFO \ -L $ExonFile

Remove the temp directory

mkdir -p ${tmp_folder}_realign

Stat ${bamtools} stats \ -insert \ -in $PWDS/${subjectID}.realigned.bam \ > $PWDS/${subjectID}.realigned.stats

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