Published November 19, 2023
| Version v1.0.0
Software
Open
Variant calling pipeline with short read sequences.
Description
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.
Contact
- Peng Jia at Xi'an Jiaotong University (pengjia@stu.xjtu.edu.cn)
Files
PengJia6/NGSGermlineMutPipe-v1.0.0.zip
Files
(32.3 kB)
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Additional details
Related works
- Is supplement to
- Software: https://github.com/PengJia6/NGSGermlineMutPipe/tree/v1.0.0 (URL)