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全外显子分析（WES）的一般步骤-5校正篇
需要校正双端信息，有时候也可以省略。
去除PCR，这个在捕获法中必须加，而在扩增子测序时，要去掉 #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 ############################################################# # Filter the results ############################################################# # filter mapping and pairing results ${bamtools} filter -isMapped true -isPaired true -isProperPair true -in $OUTPUT/${subjectID}.fxmt.bam -out $OUTPUT/${subjectID}.fxmt.flt.bam # index the BAM file ${samtools} index $OUTPUT/${subjectID}.fxmt.flt.bam #Make a temp directory mkdir -p ${tmp_folder}_rmdup #Using Picard remove duplicate java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_rmdup \ -jar ${picard}/MarkDuplicates.jar \ I\=$PWDS/${subjectID}.fxmt.flt.bam \ O\=$PWDS/${subjectID}.rmdup.bam \ M\=$PWDS/${subjectID}.duplicate_report.txt \ VALIDATION_STRINGENCY\=SILENT \ REMOVE_DUPLICATES\=true #Using Picard add group info java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_rmdup \ -jar ${picard}/AddOrReplaceReadGroups.jar \ RGLB\=${subjectID}.fastq \ RGPL\=Illumina \ RGPU\=GRP1 \ RGSM\=GP1 \ I\=$PWDS/${subjectID}.rmdup.bam \ O\=$PWDS/${subjectID}.rmdup.grp.bam \ SORT_ORDER\=coordinate \ CREATE_INDEX\=true \ VALIDATION_STRINGENCY\=SILENT #rename mv -f $PWDS/${subjectID}.rmdup.grp.bam $PWDS/${subjectID}.rmdup.bam mv -f $PWDS/${subjectID}.rmdup.grp.bai $PWDS/${subjectID}.rmdup.bai #Stat ${bamtools} stats \ -insert \ -in $PWDS/${subjectID}.rmdup.bam \ > $PWDS/${subjectID}.rmdup.stats #Remove the temp directory rm -rf ${tmp_folder}_rmdup |
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