Filter

= Filter = Filtering for mapping, pairing, and proper paired

Using bamtools filter ${bamtools} filter \ -isMapped true \ -isPaired true \ -isProperPair true \ -in $PWDS/${subjectID}.fxmt.bam \ -out $PWDS/${subjectID}.fxmt.flt.bam

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

Indexing ${samtools} index $PWDS/${subjectID}.fxmt.flt.bam

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