#!/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