Fixmate

= Fixmate = Fixing the mate pairs information. Ensure that all mate-pair information is in sync between each read and it's mate pair. Make a temp directory mkdir -p ${tmp_folder}_fixmate Using Picard fixmate java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_fixmate \ -jar ${picard}/FixMateInformation.jar \ INPUT\=$PWDS/${subjectID}.srt.bam \ OUTPUT\=$PWDS/${subjectID}.fxmt.bam \ SO\=coordinate \ CREATE_INDEX\=true \ VALIDATION_STRINGENCY\=SILENT Generate stat ${bamtools} stats \ -insert \ -in $PWDS/${subjectID}.fxmt.bam \ > $PWDS/${subjectID}.fxmt.stats Remove the temp directory rm -rf ${tmp_folder}_fixmate

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