Tutorial:Apply beagle5.0 to make imputation and phasing under CentOS and PBS
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3.5 years ago
Shicheng Guo ★ 9.2k

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

beagle 5.0 Tutorial • 1.9k views
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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,

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