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Copy number calling and variant classification using targeted short read sequencing
Singularity port of HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (HLA-A, -B, -C)
R package – HLA Genotype Imputation with Attribute Bagging (development version only)
A series of tools and pipelines for genotyping MHC / HLA genes and alleles using SMRT Sequencing
R package specialized in HLA typing clustering and visualization based on specific similarity metrics
Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute
HLA-TAPAS pipeline for HLA association and fine-mapping studies
A structural variation pipeline for short-read sequencing
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflo…
This Snakemake pipeline implements the GATK best-practices workflow
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
Official code repository for GATK versions 4 and up
hla-mapper was designed to minimize alignment bias for HLA genes and the hg38 reference genome.
kir-mapper is a toolkit for calling SNPs, alleles, and haplotypes for KIR genes from short-read second-generation sequencing (NGS) data.
🗻 Fuji plot—a circos representation of multiple GWAS results— 🗻
gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
Rapid standardisation and quality control of GWAS or QTL summary statistics
A nextflow pipeline to perform state-of-the-art genome-wide association studies.
A Nextflow Genome-Wide Association Study (GWAS) Pipeline
Scripts for GWAS association and metaanalysis
Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data
A Nextflow workflow for HLA typing using HLA-HD