DNA_mutation_analysis
Fastqc_trim_bwa_gatk4_mutect2_HC_freebayes_annovar_pipeline
git init
git add README.md
git commit -m "DAN commit"
git status
git push -u origin master
git branch my-branch
git checkout my-granch
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perl Fastqc_bwa_gatk4_Mutect2_HC_freebayes_annovar_v3.2.pl
Usage:
eg:
perl Fastqc_bwa_gatk4_Mutect2_HC_freebayes_annovar_v3.2.pl -fq1 /home/fuzl/project/demo/demo_1.fq -fq2 /home/fuzl/project/demo/demo_2.fq -outdir /home/fuzl/project/demo/GATK4demo -gatktype 1 -vf 10
Function: Template for Perl FASTQC BWA GATK pipeline .
Command:
-fq1 str fq1 fastq format *_1.fq or _1.fq.gz
-fq2 str fq2
-outdir str outdir
-detail_cfg str detail cfg [config/detail_cfg.txt]
-gatktype INT gatk type, 1=HaplotypeCaller, 2=Mutect2 ,4=freebayes [4]
-bed str bed file
-fusion
-onlyprintcmd
-help
Author: Zhiliang Fu [email protected], QQ:594380908
Version: v1.0
Update: 2018/8/8
Version: v2.0
Update: 2019/2/27
Notes:
添加 mutect2
添加fusion
添加检查是否执行sh，有.sh.finish 时则不执行该shell
GATK 拆分多个shell
线程，内存，融合，参数外置
修改runcmd，添加报错中断机制
添加Summary
修改annovar注释版本
Version: v3.0
Update: 2019/7/26
配置文件外置
添加freebayes
qualimap 加-sd ,考虑dup
Version: v3.1
SE 的fusion_bed加都配置文件
SE 线程外置
Summary添加target bases
Version: 3.2
Update: 2019/8/10
freebayes bed 用bedtools 拆分，设置最大拆成10份
计算mapping bases 用去重后的数据