Beagle 4.1 imputation

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5.3 years ago

cetin.m ▴ 50

I am running Beagle 4.1 to impute SNPs in human WGS data.

I ran chr 21 and it took 10 days. (with ~1M markers in the ref panel)

That means the whole genome would take 2 years..

How do other people manage this?

imputation • 2.1k views

ADD COMMENT • link updated 5.3 years ago by Biostar 20 • written 5.3 years ago by cetin.m ▴ 50

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What are the specifications of your computer system? Imputation is a compute-intensive task.

ADD REPLY • link 5.3 years ago by Kevin Blighe 87k

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It is a server with 200BG ram. and here is the cpu:

Architecture: x86_64

CPU op-mode(s): 32-bit, 64-bit

CPU(s): 32

Thread(s) per core: 2

Core(s) per socket: 8

Socket(s): 2

Model name: Intel(R) Xeon(R) CPU E5-2640 v2 @ 2.00GHz

CPU MHz: 2299.921

ADD REPLY • link 5.3 years ago by cetin.m ▴ 50

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Thanks - seems that you have more than enough power. Can you take a look at my answer here to ensure that you are running it correctly? - A: Running Beagle for imputation

You are allocating enough memory via -Xmx, right?

ADD REPLY • link 5.3 years ago by Kevin Blighe 87k

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