Overview
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.
License terms
HLAscan software is freely available for academic purposes and a license is required for commercial download and installation. Please contact service@syntekabio.com for questions regarding the license.
Updates
(1) HLAscan v2 is compatible with human reference (hg19(v37) and v38).
(2) Bam file and Fastq files can get to as an HLAscan v2 input.
(3) Increase the ease of use.
(4) Optimizations
HLAscan v2 uses Suffix Array (SA) method instead of BWA-mem for alignment with IMGT/HLA Database.
Contents
(1) DB
HLA-ALL.IMGT : IMGT/HLA database
(2) Tool
hla_scan_r_v2.1.4
Usage
(1) Download the DB & Tool
(2) Read Manual
./hla_scan
(3) Execute the tool
./hla_scan –b [Bam file] –v [37/38] –d [DB] –g [Gene Symbol] –t [# of threads]
./hla_scan –l [fastq file] (-r [fastq file2]) –v [37/38] –d [DB] –g [Gene Symbol] –t [# of threads]
Commands
(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]
Options
(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
You can download programs from the links underneath or from the release page
HLAscan v2.1.4
HLAscan v2.1.4
HLAscan v2.1.3 (An error in specific case is fixed.)
HLAscan v2.1.3
HLAscan v2.1.2 (An error in specific case is fixed.)
HLAscan v2.1.2
HLAscan v2.1.1
HLAscan v2.1.1
HLAscan v2.1.0
HLAscan v2.1
HLAscan v2.0
HLAscan v2.0 Manual.pdf [Files: HLAscan v2.0]
HLAscan v1.0
HLAscan v1.0 Manual.pdf [Files: HLAscan v1.0 Files.zip]
You can download the dataset from here.