Question: Beagle Imputation Markers List
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avik • 60 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.
Try using the low memory flag. That solved my Beagle problems. I think lowmem should be the default, but I am biased.
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) ?