HLA-TAPAS

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HLAassoc

3

Thank u for creating this amazing tool! I have two questions. 1. How does HLA-TAPAS deal with the multiallele situation in logistic regression model(HLA alleles，two field)? 2. If I impute...

jhylwq123

Beagle 5 difference

1

Hi, Would there be a problem with the calculation or output if I replace Beagle 4.1 for version 5, which is much faster?

jumoline

This PR improves error handling by following the recommendation in the [python documentation](https://docs.python.org/3/library/os.html#os.system). Now the execution halts when ever a command returns an error code. Additionally, I fixed an error...

nmendozam

HLAassoc > Omnibus Test

2

I want to try omnibus test and I am wondering how the .bim file of reference panel should look like, should all the AA that are on the same position...

DelnazRoshandel

Inconsistent marker IDs - Self-made 1kg subset

1

Hello, First of all thank you for your efforts in making this software :) I am currently having an issue when I am attempting to use MakeReference to make my...

erichards52

Hi, I have been using Michigan server to impute HLA variants on Four-digital V2 panel, while I notice that there are some ""duplicated" Amino Acids that only differ with an...

shudanhua

Hi, I want to apply your algorithm to the data output from SNP2HLA, but I realized that the vcf file your specified doesn't really match what I got from SNP2HLA....

xiw588

We have noticed some samples have 3 allele results for DPA1 or HLA-A genes for example. We are using the 4 digit HLA analysis tool within Michigan for the analysis....

Thenusha1

What arguments should I pass to pass to run in exhaustive mode?

1

Hi @WansonChoi, Thanks for your piece of software. I'd like to run the omnibus test in exhaustive mode. However, it's not clear to me what needs passing to the --exhaustive...

sahwa

Error: "Exception in thread "main" java.lang.StackOverflowError"

7

Hi @WansonChoi , I get an error when I run “SNP2HLA”. Can you help me see what's wrong? （There are 14390 samples） My overall commmand is like this ######################################## `python...

kaqisekuzi