HLA-VBSeq statistics

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HLA-VBSeq specifications


Unique identifier OMICS_10903
Name HLA-VBSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Read data (FASTQ), or read data aligned to GRCh37/hg19 in BAM format
Input format FASTQ, BAM
Output data HLA types estimated from sequencing data
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for HLA-VBSeq

HLA-VBSeq citations


The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Genome Biol
PMCID: 5406920
PMID: 28449694
DOI: 10.1186/s13059-017-1207-1

[…] also amino acids by using two European reference panels, one based on data from HapMap-CEPH (90 individuals), and the other on the Type 1 Diabetes Genetics Consortium (T1DGC) study []. Another tool, HLA-VBSeq, allows imputation of MHC alleles at full resolution from whole-genome sequence data []. HLA-VBSeq does not require prior knowledge of MHC allele frequencies and can therefore be used for sa […]


Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications

PMCID: 4919381
PMID: 27283945
DOI: 10.1007/s12015-016-9662-8

[…] between individuals that may have predictive value. In addition, as we have shown in the results, WGS provides significant additional value. We, for example, used standard software tools (BOOGIE and HLA VBSeq) to infer minor blood group antigens and high-resolution HLA typing. This information is difficult to assess without expensive tests and is not done routinely; the WGS if performed on iPSC c […]


Rare variant discovery by deep whole genome sequencing of 1,070 Japanese individuals

Nat Commun
PMCID: 4560751
PMID: 26292667
DOI: 10.1038/ncomms9018

[…] an genome, and their haplotype structures are different among human populations. In this study, we have typed HLA alleles of HLA-A, HLA-B and HLA-C loci of 1KJPN using newly developed software called HLA-VBSeq. The method is based on the alignment of sequence reads to the genomic HLA allele sequences registered in the IMGT/HLA database. We successfully typed HLA-A alleles for most of the individua […]


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HLA-VBSeq institution(s)
Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
HLA-VBSeq funding source(s)
This work was supported (in part) by MEXT Tohoku Medical Megabank Project.

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