WansonChoi

@DelnazRoshandel @catheriz HLAassoc uses PLINK logistic/linear regression. @DelnazRoshandel I'm sorry for the late checking. HLAassoc takes imputed VCF as input, so the former, dosage/genotype probabilities, is right.

@kaqisekuzi Hi, kaqisekuzi. Thank you for your interest in HLA-TAPAS. Could you try it again by adding "-Xss1g" after the `"-Xmx"+_mem` element of the `BEAGLE` variable? (https://github.com/immunogenomics/HLA-TAPAS/blob/a2bd506b9968611f571329c3978af4e939dc3254/SNP2HLA/SNP2HLA.py#L135) Your log file...

@kaqisekuzi The "OutOfMemoryError" is probably related to the heap memory size which you allocated with the '--mem' argument. Maybe you should allocate more memory size than 160g to impute 14,390...

@kaqisekuzi I thought you were mainly interested in imputing HLA type. Why don't you try the HLA-TAPAS in the Michigan imputation server?. It might provide enough computing resource that can...

I rechecked running the example data on my system and It worked fine. So, I guess this maybe due to different system setting. Can you tell me what is your...

@brettva Hi I checked this issue last night. I didn't realize github doesn't notify me unless referenced by '@' though new issue is opened. Above all, I do appreciate your...

@brettva > So your approach would take out the A,T coding in the VCF for bialleleic sites and let it stay A,P in the VCF? If so I think that...

@brettva Sorry for my one confusion. I thought I introduced the 'resources/1000G.bglv4.bgl.phased.vcf.gz' data, but Yang Luo did it (https://github.com/immunogenomics/HLA-TAPAS/commit/db6dec600fd544e5151cf2be8790784fde94a507#diff-41d311a605520fc7b8b9a980a79437a26e26cebcbfdd569dd78d30f7cb3e7237). I was confused because I have created a similar 1000G reference...