Software

GAT

GAT is a generic tool for conducting GWAS(Genome-Wide Association Study) on phased/unphased(=dosage) biallelic/multiallelic markers simultaneously.

GAT is a generic tool for conducting GWAS(Genome-Wide Association Study) on phased/unphased(=dosage) biallelic/multiallelic markers simultaneously.

Chanwoo Kim, Young Jin Kim, Wanson Choi, Hye-Mi Jang, Mi Yeong Hwang, Sunwoo Jung, Hyunjoon Lim, Sang Bin Hong, Kyungheon Yoon, Bong-Jo Kim, Hyun-Young Park, Buhm Han. "Phenome-wide association study of the major histocompatibility complex region in the Korean population identifies novel association signals." Human Molecular Genetics, 31(15):2655-2667. 2022

Keyword: #GWAS, #PheWAS, #HLA
CookHLA

CookHLA imputes HLA genes and amino acids from SNP genotype data.

CookHLA imputes HLA genes and amino acids from SNP genotype data.

S. Cook, W. Choi, H. Lim, Y. Luo, K. Kim, X. Jia, S. Raychaudhuri and Buhm Han, “CookHLA: Accurate Imputation of Human Leukocyte Antigens”. Nature Communications. 2021.

Keyword : #HLA, #imputation, #snp2hla
PLEIO

PLEIO offers a summary-statistic-based framework to map and interpret pleiotropic loci in a joint analysis of multiple traits.

PLEIO offers a summary-statistic-based framework to map and interpret pleiotropic loci in a joint analysis of multiple traits.

Lee, Cue Hyunkyu, Huwenbo Shi, Bogdan Pasaniuc, Eleazar Eskin, and Buhm Han. “PLEIO: a method to map and interpret pleiotropic loci with GWAS summary statistics.” The American Journal of Human Genetics 108, no. 1 (2021): 36-48.

Keyword : #pleiotropic, #meta-analysis
HATK

HATK imputes HLA genes and amino acids from SNP genotype data.

HATK imputes HLA genes and amino acids from SNP genotype data.

Wanson Choi, Yang Luo, Soumya Raychaudhuri, Buhm Han. “HATK:HLA-Analysis Tool-kit” Bioinformatics. 2020.

Keyword : #HLA, #imputation
GenomicGPS

Genomic GPS: using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes

Genomic GPS: using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes

Kunhee Kim, Hyungryul Baik, Chloe Soohyun Jang, Jin Kyung Roh, Eleazer Eskin, Buhm Han. “Genomic GPS: using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes” Genome Biology (2019) 20:175

Keyword : #privacy, #genetic_distance
mergeReference

MergeReference merges multiple reference panels for HLA imputation. The merged reference panel could be used for running CookHLA and SNP2HLA.

MergeReference merges multiple reference panels for HLA imputation. The merged reference panel could be used for running CookHLA and SNP2HLA.

Cook, Seungho, and Buhm Han. “MergeReference: a tool for merging reference panels for HLA imputation.” Genomics & Informatics 15, no. 3 (2017): 108.

Keyword : #HLA, #imputation, #mergereference