hla-mapper
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The polymorphic nature of most HLA genes and their high sequence similarity lead to read mapping bias and genotyping errors. hla-mapper was designed to minimize these issues. Based on a database of known HLA sequences, each read pair is scored and addressed to the most likely locus. The final output is a BAM file with reads mapped to the human reference genome (version hg38), allowing any downstream analysis that suits the user. The resulting BAM file is far more reliable than those generated by using BWA, Bowtie2, or other mapping tools directly
Download it on GitHub
Check the manuscript introducing this package.
Where it was first described: Hum Immunol. 2018 Sep;79(9):678-684.
kir-mapper
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kir-mapper is a toolkit for calling SNPs, alleles, and haplotypes for KIR genes from short-read second-generation sequencing (NGS) data. kir-mapper supports both single-end and paired-end Illumina sequencing data. It is compatible with Ion Torrent data uppon some adjustments.
Download it on GitHub
Check the manuscript introducing this package.
Where it was first described: HLA. 2025 Mar;105(3):e70092. doi: 10.1111/tan.70092.
VCFx
- VCFx comprises a set of tools for handling VCF (Variant Call Format) files, including converting phased VCF in complete fasta sequences. Download it on GitHub