Create intervals

= Create Intervals = Collect regions around potential indels and clusters of mismatches. Determine small suspicious intervals which are likely in need of realignment.

Make a temp directory mkdir -p ${tmp_folder}_realign

Using GATK to create intervals java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_realign \ -jar $gatk \ -T RealignerTargetCreator \ -I $PWDS/${subjectID}.mq.srt.bam \ -R $REF \ -known $DBSNP \ -nt $CPUs \ -o $PWDS/${subjectID}.forRealign.intervals  \ -L $ExonFile

Remove the temp directory rm -rf ${tmp_folder}_realign

< Back to Whole Exome Sequencing Analysis Pipeline