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TGSGermlineMutPipe

Germline mutations detection pipeline for long reads

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

Support tools

  • deepvaraint
  • cuteSV
  • sniffles
  • pbsv
  • SVision
  • ...

Contribution

If you want to apply other tools to mutations with long 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

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