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全外显子分析（WES）的一般步骤-4 对比篇
用BWA，双端比对
#Paired-end first batch echo "pe alignment " $bwa sampe \ $hg19_ref \ $PWDS/fastq1.sai \ $PWDS/fastq2.sai \ $fastq_path1/$fastq_for_gz \ $fastq_path1/$fastq_rev_gz \ | gzip > $PWDS/${subjectID}.sam.gz \ 2> PWDS/${subjectID}.pe.log #Sorting bam ${samtools} view -uS $PWDS/${subjectID}.sam.gz \ | ${samtools} sort -m 3000000000 - $PWDS/${subjectID}.srt #Indexing bam ${samtools} index ${PWDS}/${subjectID}.srt.bam #Generate stat ${bamtools} stats \ -insert \ -in $PWDS/${subjectID}.srt.bam \ > $PWDS/${subjectID}.srt.stats |
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