Cleanup

= Cleanup = Remove all intermediate alignment and BAM files. Keep only first aligned and last realigned-recalibrated BAM files.

rm -rf ${PWDS}/alignments rm -rf ${PWDS}/${subjectID} rm -rf ${PWDS}/${subjectID}.srt.bam rm -rf ${PWDS}/${subjectID}.srt.bam.bai rm -rf ${PWDS}/${subjectID}.fxmt.bai rm -rf ${PWDS}/${subjectID}.fxmt.bam rm -rf ${PWDS}/${subjectID}.fxmt.flt.bam rm -rf ${PWDS}/${subjectID}.fxmt.flt.bam.bai rm -rf ${PWDS}/${subjectID}.rmdup.bam rm -rf ${PWDS}/${subjectID}.mq.bam rm -rf ${PWDS}/${subjectID}.mq.fxmt.bai rm -rf ${PWDS}/${subjectID}.mq.fxmt.bam rm -rf ${PWDS}/${subjectID}.mq.srt.bai rm -rf ${PWDS}/${subjectID}.mq.srt.bam rm -rf ${PWDS}/${subjectID}.flt.recal_v1.csv rm -rf ${PWDS}/${subjectID}.flt.recal_v2.csv rm -rf ${PWDS}/${subjectID}.forRealign.intervals rm -rf ${PWDS}/${subjectID}.realigned.bam rm -rf ${PWDS}/${subjectID}.realigned.fxmt.bai rm -rf ${PWDS}/${subjectID}.realigned.fxmt.bam

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