A web for GenePanel build with core of Nextflow.
Key Features • How To Use • Main Workflow • Credits •
- Save the result preview as PDF
- Cross platform
- Linux ready.
- docker ready
To clone and run this application, you'll need Git and Java
# Install nextflow
$ mkdir genepanel
$ cd genepnel
$ curl -s https://get.nextflow.io | bash
$ ./nextflow run hello
# Clone this repository dowload annovar database (location gene panel)
$ git clone https://github.com/liesyx/Gene-Panel.git
$ export PATH=/data/annovar/annovar:$PATH
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb avsnp150 -buildver hg38 data/annovar/annovar/humandb
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb gnomad312_genome -buildver hg38 data/annovar/annovar/humandb
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb cosmic70 -buildver hg38 data/annovar/annovar/humandb
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb refGene -buildver hg38 data/annovar/annovar/humandb
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb cytoBand -buildver hg38 data/annovar/annovar/humandb
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb clinvar_20221231 -buildver hg38 data/annovar/annovar/humandb
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb intervar_20180118 -buildver hg38 data/annovar/annovar/humandb
$ perl data/annovar/annovar/annotate_variation.pl -webfrom annovar -downdb hrcr1 -buildver hg38 data/annovar/annovar/humandb
# build docker imgaes
$ docker build -t genepanel:latest .
# Run the app (high recomment) (the location of fastqc.nf file )
$ ./nextflow run fastqc.nf --reads link_your_reads/*{1,2}.f* -with-docker genepanel
# website for developer
$ uvicorn main:app --host 0.0.0.0 --port 8888 --reload# Parameter
# -resume
# -NM_data_
# -bed_file
# -ten_du_an
# -goitinh
# -ngaynhanmau
# -tenkhachang
# -adapter_dir
This software uses the following open source packages:
