Question: Beagle imputation output, incorrect genotype probability format?
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gravatar for Tails
4.3 years ago by
Tails30
New Zealand
Tails30 wrote:

After imputing with BEAGLE one of the markers (a deletion) doesn't have three genotype probabilities but instead just has a '1' written in its place.. usually there are three comma separated probabilities.. does anyone know if this is a bug in BEAGLE?

##INFO=<ID=AR2,Number=1,Type=Float,Description="Allelic R-Squared: estimated correlation between most probable ALT dose and true ALT dose">
##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated correlation between estimated ALT dose [P(RA) + 2*P(AA)] and true ALT dose">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="estimated ALT dose [P(RA) + P(AA)]">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Estimated Genotype Probability">

CHR    POS              ID      REF  ALT   QUAL FILTER INFO                   FORMAT         1111    2222   3333   4444

Chr1    51058623        .       A       .       .       PASS    AR2=0;DR2=0     GT:DS:GP        0|0:0:1 0|0:0:1 0|0:0:1 0|0:0:1

beagle imputation sequence • 2.0k views
ADD COMMENTlink written 4.3 years ago by Tails30
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