lizhonggang1984 / locuszoom

This folder includes all files needed to conduct locuszoom plot based on mouse and human GWAS files. You need GWAS file with pValue and rsID (or SNP position).

LocusZoom

download required software and intalled in Linux environment

https://genome.sph.umich.edu/wiki/LocusZoom_Standalone

(1) install python and R in linux system (2) install new_fugue and plink for LD calculation (3) download the full folder of locuszoom (including all data files with LD files) to drive, untar all files

In Attie-VM, all software has been installed

Our Locuszoom is in attie-vm at :

/mnt/data/locuszoom

To use mouse data, follow next steps

(1)go the example folder (2) use the Python script for analysis. If change the path, go to conf folder and change the configure file.

we already updated mm10 to .db: bin/lzupdate.py --build mm10

using conf/m2z.config file to change your configuration

To run LocusZoom to draw mouse genome locuszoom, use six steps:

(1) log in into Attie-VM (2)$ ls $ sudo su $ (YOURpassword) $ cd /mnt/data/locuszoom/examples (3) // conduct shell to setup path for tabix for LD calculation export PATH=$PATH:/mnt/data/locuszoom/tabix-0.2.6

(4) //upload mouse gwas file to the example folder

this text file must have at least two columns,
MarkerName and P-value (column name should be exactly these two)

(5) // edit python file to perform locuszoom // to calculate LD, using mouse_vcf.py to do it

change --refsnp to your snp and change --flank to 200kb or 500kb as needed

(6) //conduct ./mouse_vcf.py to draw plots

./mouse_vcf.py or ./mouse_no_ld.py (if not using LD block) or ./mouse_hapmap.py (if using hapmap data for LD calculation)

To run LocusZoom to draw human genome locuszoom, use six steps:

(1) log in into Attie-VM (2)$ ls $ sudo su $ (YOURpassword) $ cd /mnt/data/locuszoom/gwas (3) // conduct shell to setup path for tabix for LD calculation export PATH=$PATH:/mnt/data/locuszoom/tabix-0.2.6

(4) //upload human gwas file to the example folder

this text file must have at least two columns,
MarkerName and P-value (column name should be exactly these two)

(5) // edit python file to perform locuszoom // to calculate LD, using our scripted python script to do it

change --refsnp to your snp and change --flank to 200kb or 500kb as needed

(6) //conduct human gwas plot to draw plots

./glgc_exometc.py
or other related python file (modify file folder and name to draw plots)