Question: How to get "best guess" genotypes after running Beagle 4.1
0
gravatar for vmuir
2.2 years ago by
vmuir0
vmuir0 wrote:

Hi all. I've run Beagle v4.1 imputation for a bunch of samples, and one of my collaborators would like to use the best-guess SNP calls rather than the dosages/probabilities. I haven't had luck finding out how to get this data (short of running Beagle 3.3 or IMPUTE2/Minimac) online or in the beagle manual. What's the best way to extract this data?

Here's what my data currently look like:

17  37500884    rs71147320  C   CA  .   PASS    AR2=0.19;DR2=0.26;AF=0.26;IMP   GT:DS   0|1:0.6 1|1:1.32    0|0:0.2 0|1:0.94    1|0:0.84    0|1:0.67    0|1:0.88    0|0:0.25    0|0:0.22    1|0:0.89    0|0:0.19    0|0:0.25    0|0:0.29    0|0:0.29    1|0:0.73    0|0:0.48    0|0:0.34    0|0:0.44    0|0:0.35    0|0:0.3 0|1:1.02    0|0:0.41    0|0:0.24    0|0:0.32    0|0:0.17    0|0:0.13    1|1:1.34    0|1:0.71    0|0:0.1 0|0:0.26    0|0:0.48    0|1:0.78    0|1:0.69    0|0:0.59    0|0:0.18    0|0:0.26    0|0:0.16    1|0:0.73    0|0:0.18    0|0:0.26    0|1:0

Thanks!

beagle imputation • 743 views
ADD COMMENTlink written 2.2 years ago by vmuir0

The most likely genotype configuration is the two numbers separated by the pipe "|" symbol, for example, the most likely configuration at the first individual is 0|1, a homozygote, and 0|0, a homozygote at the second individual.

ADD REPLYlink written 2.2 years ago by 4galaxy7780
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