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全外显子组生信分析流程-7-depth_and_coverage_qualimap
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#!/usr/bin/bash #!/usr/bin/bash #purpose: calculate deapth and coverage using Qualimap ## Download and install Qualimap ## http://qualimap.bioinfo.cipf.es/ #安装 cd /home/zhanghl/supporting_softwares mkdir qualimap && cd qualimap wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip ## readme http://qualimap.bioinfo.cipf.es/doc_html/index.html ## example results :http://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html /home/zhanghl/supporting_softwares/qualimap/qualimap_v2.2.1/qualimap --help #运行 #set env bam_dir=" " /home/zhanghl/supporting_softwares/qualimap/qualimap_v2.2.1/qualimap bamqc --java-mem-size=20G -bam $bam_dir/P1-01-DNA.sorted.dedup.bam -nw 400 -hm 3
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