Question: Phasing without a reference panel
gravatar for chadapohn.chaosrikul
11 days ago by
chadapohn.chaosrikul0 wrote:

Hi all,

I'm trying to make my own cohort from genotypes like HapMap project. I would like to know if there are any phasing tools which contain options for phasing genotypes when there's no reference panel?

Thank you.

ADD COMMENTlink modified 11 days ago by Wietje60 • written 11 days ago by chadapohn.chaosrikul0
gravatar for Wietje
11 days ago by
Wietje60 wrote:

Beagle 4.0 offers the option to impute and phase without a reference panel

You should be able to run it with: java -jar ./beagle gt=[your.file.vcf] phase-its=5 nthreads=1 out=[your.output]

You can speed up the process with more threads and improve phasing accuracy by augmenting the phase-its number.

Documentation can be found here:

ADD COMMENTlink modified 11 days ago • written 11 days ago by Wietje60

And you might want to take a look at SHAPEIT as well (

ADD REPLYlink written 11 days ago by Wietje60

Thank you for your help! I'd like to know if I used SHAPEIT without a reference (by not specify --input-ref option) Does it use the default reference e.g 1000GP or use MCMC algorithm to estimate haplotypes instead?

ADD REPLYlink modified 5 days ago • written 5 days ago by chadapohn.chaosrikul0

As far as I know, you have to invoke the reference panel option with --input-ref to make use of such a panel - otherwise SHAPEIT will phase without this kind of background information. If you want to use the 1000GP data for your phasing step, you'd have to download it as described on the SHAPEIT page (also check these instructions for further parameters and input/output options:

ADD REPLYlink written 3 days ago by Wietje60
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