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nanjalaruth / MHC-Imputation-Accuracy

A project on evaluating the accuracy of genotype imputation in the human MHC region in selected African populations.
MIT License
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HLA_Type_Table #2

Open karpat90 opened 1 year ago

karpat90 commented 1 year ago

Hello!

Thank you for creating a great pipeline for assessing HLA imputation accuracy. I am planning to use HIBAG for imputing Sudanese genomes. Where I could obtain HLA_Type_Table for individuals of African ancestry? Specifically in your scripts you use:

HLA_Type_Table <- read.table(file="1kg_all_hibag_hlatypes.edited")

whereas HIBAG package uses:

data(HLA_Type_Table, package="HIBAG")

Where I could obtain 1kg_all_hibag_hlatypes.edited?

Thank you for your help!

nanjalaruth commented 1 year ago

Hi @karpat90

You have to do HLA typing first, you can use either Optitype for HLA class I only (https://github.com/nf-core/hlatyping) or HLA-LA for both HLA class I and Class II (https://github.com/nanjalaruth/hla_typing_using_HLA-LA)

karpat90 commented 1 year ago

Thank you for your prompt reply! I will use suggested tools to make HLA tables from 1000 genomes bam files.