Filter low mapping quality

= Filter low mapping quality = Filter low mapping quality reads Using bamtools filter $bamtools  filter \ -mapQuality ">=60"   \ -in  $PWDS/${subjectID}.rmdup.bam   \ -out $PWDS/${subjectID}.mq.srt.bam

Indexing $samtools index $PWDS/${subjectID}.mq.srt.bam

Generate stat ${bamtools} stats \ -insert \ -in $PWDS/${subjectID}.mq.srt.bam \ > $PWDS/${subjectID}.mq.srt.stats

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