Interpreting phased data from Beagle
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4.2 years ago

Dear all,

I'm trying to investigate how Beagle works when phasing with a reference panel and without a reference panel. I've got phased data of unrelated individuals that contain missing markers from these two commands (I'm using Beagle 3.3):

1) The first one goes with a reference panel.

java -Xmx444m -jar beagle.jar markers=./hapmap.markers phased=./hapmap.phased.bgl unphased=./hapmap.unphased.bgl missing=? out=./output

Phased data:

M rs12133813 G A G G


M rs7529536 G G G G


M rs3820577 G G G A


2) The second one goes without a reference panel.

java -Xmx444m -jar beagle.jar markers=./hapmap.markers unphased=./hapmap.unphased.bgl missing=? out=./output

Phased data:

M rs12133813 A G G G


M rs7529536 G G G G


M rs3820577 G G A G


I would like to ask you all what makes the results of two experiments different? Please give me some suggestions.

Thank you.

genotype haplotype beagle phasing imputation • 2.1k views
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Did you read the manual? - do you understand the concept of phasing in relation to genotypes?

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