HLAscan is an alignment-based program that determines haplotypes taking read distribution into account. The software performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database.
The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. HLAscan can be reliably applied for determination of HLA type across the whole-genome, exome, and target sequences.
HLAscan software is freely available for academic purposes and a license is required for commercial download and installation. Please contact email@example.com for questions regarding the license.
Ka, S., Lee, S., Hong, J., Cho, Y., ... & Jung, J. (2017). HLAscan: genotyping of the HLA region using next-generation sequencing data. BMC bioinformatics, 18(1), 258.
(1) HLA typing (input : bam file)
./hla_scan -b [bam] -d [IMGT/HLA DB] -v [version(37 or 38)]
(2) HLA typing (input : fastq files)
./hla_scan -l [fastq] (-r [fastq2]) -d [IMGT/HLA DB]
(1) Gene List -g [string], default=HLA-A
HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, MICA, MICB,
HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1,
HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB5, TAP1, TAP2
(2) Score Cutoff -s [int], default=50
(3) Constant using ScoreFunc -c [int], default=30
(4) # of threads -t [int], default=32
- HLAscan v2.1.1
- HLAscan v2.1.0
- HLAscan v2.0
- HLAscan v1.0