xmxjy 报告流程

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ip: 192.168.0.33

1.生成fastq文件

cd /workdir/data
ll
mkdir result_190422data
cd result_190422data
cp /workdir/data/result_190422/run_bcl2fastq.sh .
mkdir fastq

vim run_bcl2fastq.sh (鼠标无法操作)
按i
按 左上角的ESC  shift+:  wq   保存退出
按 左上角的ESC  shift+:  q   不保存退出

#编辑run_bcl2fastq.sh 文件,这里是要修改的
sample_sheet=030-190422.csv
bcl_name=190421_TPNB500301_0050_AHHVW2AFXY

ll /cifs/NextSeq/Runs/HIGIA/
#
nohup sh run_bcl2fastq.sh &

jobs

2. call SNP

cd /workdir/SNP_result/
mkdir newdir
cd newdir
vim list

新建 list 文件，以tab分割

image.png

-r  /workdir/data/result_190422/fastq/ 是前一步的fastq文件

perl /workdir/SNPcall_GATK/SNPcall_samtools.pl -o . -l list -r /workdir/data/result_190422/fastq/
cd script 

cp /workdir/SNP_result/zsl_samtools_20190422/1/script/run.sh .
不要修改
#检查文件是否存在
for i in `cat  */*/*filter* | grep cat | awk '{print $2}'`;do ll -h $i;done

#执行脚本
nohup sh run.sh &


#查看脚本运行状态
jobs
       running  正在运行
       done      运行完成

3.QC

#查看深度
cd ../Coverage
grep  'Average depth(rmdup)' */*/coverage.report > coverage.txt
cat coverage.txt

#查看捕获率
grep 'Fraction of Target Reads in mapped reads' */Coverage/*/*/*coverage.report

or

grep 'Fraction of Target Reads in mapped reads' */Coverage/*/*/*coverage.report | grep -v nan | awk '{sub(/%$/, " ");  if ($10 <10) print}'

#查看位点
cd ../out
wc -l */*.txt

pwd

4.数据打包

zip -r file.zip */*.txt

5.分析

#进入家目录
cd

test 是自己随意命名
mkdir test && cd test
cp -r ../mould_zhaosl/* .
cd sample

要修改
cp /workdir/SNP_result/zsl_samtools_20190422/1/out/file.zip .

unzip file.zip
rm file.zip
head -1 */*.txt

cd ../whole_test/

nohup ./run.sh &
cd ..

等待10~20分钟

查看胎儿浓度
grep -A 5 'testing the pair' whole_test/nohup.out

grep -A 5 'testing the pair' whole_test/nohup.out | perl -ne 'print "$1\t" if/testing the pair of (\w+)/; print "$1\n" if/Fraction\(fetal\)=  (\S+)/' | awk '{if( $2 != none)print }' |sort

查看杂质
for i in {2..30};do cat genotype253.txt | awk '{print $1,$2,$3,$4,$5}' | grep -w $i;done

查看结果文件
cat whole_test/Result_testing.txt