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 firstname.lastname@example.org for questions regarding the license.
Ka, Lee, et al. (A manuscript is submitted.)
hla-ref (DB) contents
Name Description exn Collection of exon boundary IMGT_HLA FASTA files for each genes (reference)
HLA gene lists files
Name Description allele_count_cpu BAM filter bwa Alignment ghaplo_scan Covert BAM files into FASTQ format haplo_scan_v4.0 Determine gene types haplo_scan_v4.0-hla.py Action script samtools Calculate a depth
- python 2.7
1.Download the files
2.Set the configuration
PROG_BAMTOFASTQ = "./ghaplo_scan"
PROG_BWA = "./bwa"
PROG_FILTEREDBAM = "./allele_count_cpu"
PROG_SAMTOOLS = "./samtools"
PROG_HLASCAN = "./haplo_scan_v4.0"
FA_FILE = "../hla-ref-5gene/IMGT_HLA/" #fixed
SGENE = "" #fixed
GENE_634 = "" #fixed
EXON_7255 = "" #fixed
GENE_BOUND = "../hla-ref-5gene/exn/"
python ./haplo_scan_v4.0-hla.py [bam] [gene list] [output path]
ex) python ./haplo_scan_v4.0-hla.py ../NA12878.5gene.bam ../hla-ref/gene_list ../test-out