Question: Beagle Imputation Markers List
gravatar for avik
7.8 years ago by
avik60 wrote:

Hi, I 'm trying to impute genotype calls using Beagle and reference panel. I have a likelihood file of genotyped markers and a list of ungenotyped markers (as Beagle documentation says "When imputing ungenotyped markers using a reference panel, the markers file should contain only the markers genotyped in the reference panel"). But execution stopped with "NullPointerException" when only ungenotyped markers were provided as input. But its not complaining when both genotyped and ungenotyped markers are present in markers file. Has anybody experienced same before or its problem with only my dataset? Any suggestion to deal with such scenario? Thanks in advance.

imputation • 3.3k views
ADD COMMENTlink modified 5.8 years ago by alexamty860 • written 7.8 years ago by avik60

Try using the low memory flag. That solved my Beagle problems. I think lowmem should be the default, but I am biased.

ADD REPLYlink written 7.8 years ago by Zev.Kronenberg11k

Thanks for reply. I have tried using that flag, but I don't think its due to memory limitation. Does your Beagle input file (like/unphased/?) also contain ungenotyped markers (not partially genotyped) ?

ADD REPLYlink written 7.8 years ago by avik60
gravatar for alexamty86
5.8 years ago by
alexamty860 wrote:

hello zev, 


Could you help me with some questions that i have with Beagle,  please I´ll appreciate this because i´m trying make an imputation of 50k to 700k,  thank you

ADD COMMENTlink written 5.8 years ago by alexamty860
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