Open afaulconbridge opened 2 years ago
@afaulconbridge
Hi, Thank you for your interest in CookHLA.
As far as I checked, the 1000G_ALL reference panel worked well with the toy example.
Could you try the imputation again with Bealge4 instead of Beagle5? (Add '-bgl4' argument.) I've seen a similar error(java.lang.IllegalArgumentException) before, but I couldn't figure out the exact cause. At least I know this error sometimes occurs in only Beagle5 and barely occurs with Beagle4.
Thanks for making this software available. I can successfully impute from the 1000G individual superpopulation files, but I'm seeing an error when I try to use the combined overall 1000G reference panel. Specifically Beagle says:
though exactly which exon raises the error doesn't seem to be consistent. Sometimes its 2.1 but also 2.1.5 too.
Have you been able to use the 100G_ALL reference successfully? Is there anything that needs to be changed or checked to work with the larger reference panel?