GemlineMutPipe

Germline mutation pipeline for Next generation sequencing analysis.

Quick start

1. change the following configure files according to you environment.

• conf/config.yaml (control the software you want to use)
• conf/reference.yaml (configure the reference you want to use)
• conf/cluster.yaml (configure the threads for each rule )
• conf/samples.yaml (configure the samples you want to run)
• rules/software.smk (configure the absolute path of your software)

2. run with snakemake

   nohup snakemake -s ngsGermlinePipe.smk -j 10 -k --ri >sublog 2>&1 &
   nohup snakemake -s ngsGermlinePipe.smk -j 10 -k --ri --cluster "qsub -l nodes=1:ppn=20 -l walltime=999:00:00" >sublog 2>&1 & 

Support tools

• gatk
• varscan
• deepvariant
• manta
• delly
• svaba
• smoove/lumpy
• pindel
• ...

Contribution

If you want to apply other tools to mutations with NGS reads, we encourage you to pull a request or email us.

Citation

Jia P, Dong L, Yang X, Wang B, Wang T, Lin J, Wang S, Zhao X, Xu T, Che Y, et al: Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet. bioRxiv 2022:2022.2009.2008.504083. PDF

Contact

• Peng Jia at Xi'an Jiaotong University (pengjia@stu.xjtu.edu.cn)