Tutorial:Apply beagle5.0 to make imputation and phasing under CentOS and PBS

Question

[Shicheng Guo]

I didn't find beagle imputation and phasing tutorial, therefore, try to give one sine I am using it right now. And hope to receive some feedback.

1. Prepare beagle 5.0 and corresponding database

   https://raw.githubusercontent.com/Shicheng-Guo/HowtoBook/master/APP/beagle5.0/Step1.Prepare.sh

2. Prepare beagle phasing reference for EUR samples (my samples are EUR samples)

   https://raw.githubusercontent.com/Shicheng-Guo/HowtoBook/master/APP/beagle5.0/Step2.reference.sh

3. Prepare PBS script to run beagle

   https://raw.githubusercontent.com/Shicheng-Guo/HowtoBook/master/APP/beagle5.0/Step3.beaglephasing.sh

4. Post-imputation filiter (DR2>0.7)

   https://raw.githubusercontent.com/Shicheng-Guo/HowtoBook/master/APP/beagle5.0/Step4.postfiltering.sh

[Raymond]

Thanks for sharing! May I ask if Beagle imputation works for more than 1 node? That is, when specify:

...
#PBS -l nodes=2:ppn=16
...

Does Beagle run on both 2 nodes with 32 threads?

Thanks! Raymond,

Answer 1

[Leon]

basic tutorial https://faculty.washington.edu/browning/beagle/run.beagle.16May19.351.example
detail pipeline step-by-step attached in https://doi.org/10.12688/wellcomeopenres.15126.1