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    满分室间质评之GATK Somatic SNV+Indel+CNV+SV（下）性能优化

    #此处是原先Manta分析SV的步骤一，生成runWorkflow.py，因为这一不步速度很快，所以串行执行 rm -f ${result}/${sn}/runWorkflow.py python ${tools.manta} \ --normalBam ${result}/${sn}NC_marked.bam \ --tumorBam ${result}/${sn}_marked.bam \ --referenceFasta ${refs.hum} \ --exome \ --callRegions /opt/ref/projects/Illumina_pt2.bed.zip \ --runDir ${result}/${sn} # 对bam文件碱基质量校正的第二步，Normal & Tumor并行处理 ${tools.gatk} ApplyBQSR \ --bqsr-recal-file ${result}/${sn}_recal.table \ -L ${refs.interval} \ -R ${refs.hum} \ -I ${result}/${sn}_marked.bam \ -O ${result}/${sn}_bqsr.bam & ​ ​ ${tools.gatk} ApplyBQSR \ --bqsr-recal-file ${result}/${sn}NC_recal.table \ -L ${refs.interval} \ -R ${refs.hum} \ -I ${result}/${sn}NC_marked.bam \ -O ${result}/${sn}NC_bqsr.bam & ​ #原先QC步骤，获取insert size，Normal & Tumor并行 ${tools.gatk} CollectInsertSizeMetrics \ -I ${result}/${sn}_marked.bam \ -O ${result}/${sn}_insertsize_metrics.txt \ -H ${result}/${sn}_insertsize_histogram.pdf & ​ ​ ${tools.gatk} CollectInsertSizeMetrics \ -I ${result}/${sn}NC_marked.bam \ -O ${result}/${sn}NC_insertsize_metrics.txt \ -H ${result}/${sn}NC_insertsize_histogram.pdf & ​ # 运行manta SV分析 python ${result}/${sn}/runWorkflow.py -m local -j ${envis.threads} & ​ # 运行cnvkit CNV分析 ${tools.cnvkit} batch \ ${result}/${sn}_marked.bam \ --normal ${result}/${sn}NC_marked.bam \ --method hybrid \ --targets ${refs.bed} \ --annotate /opt/ref/refFlat.txt \ --output-reference ${result}/${sn}_reference.cnn \ --output-dir ${result}/ \ --diagram \ -p 0 & ​ #samtools统计测序深度 ${tools.samtools} depth -b ${refs.bed} ${result}/${sn}_marked.bam > ${result}/${sn}_marked.depth & ${tools.samtools} depth -b ${refs.bed} ${result}/${sn}NC_marked.bam > ${result}/${sn}NC_marked.depth & #samtools统计比对信息 ${tools.samtools} flagstat --threads ${envis.threads} ${result}/${sn}_marked.bam > ${result}/$

    01

    Install Jumpserver42

    Copying '/opt/jumpserver/apps/static/js/plugins/inputTags.jquery.min.js' Copying '/opt/jumpserver/apps/static/js/plugins/cropper/cropper.min.js' Copying '/opt/jumpserver/apps/static/js/plugins/datatables/datatables.min.js' Copying '/opt/jumpserver/apps/static/js/plugins/datatables/pdfmake.min.js.map' Copying '/opt/jumpserver/apps/static/js/plugins/datatables/i18n/English.lang' Copying '/opt/jumpserver/apps/static/js/plugins/datatables/i18n/zh-hans.json' Copying '/opt/jumpserver/apps/static/js/plugins/datepicker/bootstrap-datepicker.js' Copying '/opt/jumpserver/apps/static/js/plugins/demo/peity-demo.js' Copying '/opt/jumpserver/apps/static/js/plugins/dropzone/dropzone.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/echarts-all.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/echarts.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/bar.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/chord.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/eventRiver.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/force.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/funnel.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/gauge.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/heatmap.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/k.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/line.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/map.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/pie.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/radar.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/scatter.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/tree.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/treemap.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/venn.js' Copying '/opt/jumpserver/apps/static/js/plugins/echarts/chart/wordCloud.js' C

    02

    Install Jumpserver43

    Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/modules/heatmap.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/modules/heatmap.src.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/modules/no-data-to-display.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/modules/no-data-to-display.src.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/modules/solid-gauge.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/modules/solid-gauge.src.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/dark-blue.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/dark-green.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/dark-unica.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/gray.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/grid-light.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/grid.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/sand-signika.js' Copying '/opt/jumpserver/apps/static/js/plugins/highcharts/themes/skies.js' Copying '/opt/jumpserver/apps/static/js/plugins/iCheck/icheck.min.js' Copying '/opt/jumpserver/apps/static/js/plugins/jstree/jstree.min.js' Copying '/opt/jumpserver/apps/static/js/plugins/layer/layer.js' Copying '/opt/jumpserver/apps/static/js/plugins/layer/skin/layer.css' Copying '/opt/jumpserver/apps/static/js/plugins/layer/skin/default/icon-ext.png' Copying '/opt/jumpserver/apps/static/js/plugins/layer/skin/default/icon.png' Copying '/opt/jumpserver/apps/static/js/plugins/layer/skin/default/loading-0.gif' Copying '/opt/jumpserver/apps/static/js/plugins/layer/skin/default/loading-1.gif' Copying '/opt/jumpserver/apps/static/js/plugins/layer/skin/default/loading-2.gif' Copying '/opt/jumpserver/apps/static/js/plugins/magnific/jquery.magnific-popup.min.js' Copying '/opt/jumpserver/apps/static/js/plugins/metisMenu/jquery.metisMenu.js' Copying '/opt/jumpserver/apps/static/js/plugins/pace/pac

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