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#!/usr/bin/bash #Control-Freec 既可以检测拷贝数变异CNV,还可以分析杂合性缺失LOH。官网如下 #http://boevalab.com/FREEC/ #https://www.jianshu.com/p/122cc5b4ca46 #简书https://www.jianshu.com/p/122cc5b4ca46 #官网+作图 http://boevalab.com/FREEC/tutorial.html#GCP #第一步安装 https://github.com/BoevaLab/FREEC/releases #第二步执行 /home/zhanghl/supporting_softwares/Control-Freec/FREEC-11.5/src/freec -conf /home/zhanghl/supporting_softwares/Control-Freec/FREEC-11.5/data/config_exome.txt #第二步编辑配置文件 [general] chrLenFile = /home/zhanghl/supporting_files/Homo_sapiens_hg19/hg19.fa.fai window = 0 ploidy = 2 outputDir = /home/zhanghl/data_3/workshop/practice1_ovary/control-freec/ BedGraphOutput = TRUE #sex=XY breakPointType=4 chrFiles = /home/zhanghl/supporting_files/Homo_sapiens_hg19/hg19_chromosomes/chromosomes maxThreads=6 breakPointThreshold=0.8 noisyData=TRUE printNA=FALSE readCountThreshold=50 [sample] mateFile = /home/zhanghl/data_3/workshop/practice1_ovary/raw_data/SRR5141046.sorted.dedup.recal.bam inputFormat = BAM mateOrientation = 0 [control] mateFile = /home/zhanghl/data_3/workshop/practice1_ovary/raw_data/SRR5141045.sorted.dedup.recal.bam inputFormat = BAM mateOrientation = 0 [BAF] SNPfile = /home/zhanghl/supporting_files/Homo_sapiens_hg19/hg19_snp142.SingleDiNucl.1based.txt minimalCoveragePerPosition = 5 [target] captureRegions = /home/zhanghl/supporting_files/Homo_sapiens_hg19/truseq-exome-targeted-regions-manifest-v1-2.bed #这个文件公司提供? #mpileup #samtools mpileup \ #-gSDf /home/zhanghl/supporting_files/Homo_sapiens_hg19/hg19.fa \ #/home/zhanghl/data_3/workshop/practice1_ovary/raw_data/SRR5141046.sorted.dedup.recal.bam > \ #/home/zhanghl/data_3/workshop/practice1_ovary/raw_data/SRR5141046.sorted.dedup.recal.bcf #Visualize Control-FREEC's output #If you work with Exome-seq data and you did not set printNA=FALSE, delete data points that are not in targeted regions from *_ratio.txt: awk '$3!=-1 {print}' ./P4-01-DNA.sorted.dedup.recal.bam_ratio.txt > ./P4-01-DNA.sorted.dedup.recal.bam_ratio.txt.NONA cat /home/zhanghl/data_3/biosoft/anaconda2/envs/Control-FREEC/bin/makeGraph.R | R --slave --args 2 ./P4-01-DNA.sorted.dedup.recal.bam_ratio.txt.NONA
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