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  • HLAscan Introduction

    1.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.

         2.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.

         3.Cyting HLAscan

          Ka, Lee, et al. (A manuscript is submitted.)


 

 

  • HLAscan download/Installation

    1.Contents 

    1. hla-ref (DB) contents

      NameDescription
      exnCollection of exon boundary
      IMGT_HLAFASTA files for each genes (reference)

      Gene_list

      HLA gene lists files

         

    2. tool

      NameDescription
      allele_count_cpuBAM filter
      bwaAlignment
      ghaplo_scanCovert BAM files into FASTQ format
      haplo_scan_v4.0Determine gene types
      haplo_scan_v4.0-hla.pyAction script
      samtoolsCalculate a depth

 

  1. Files : hla-paper-tools-5gene.tgz / hla-ref.tar/ NA12878.5gene.bam / NA12878.5gene.bam.bai

 

         2.Installation environment

           - python 2.7

         3.Usage  

  ⅰ) Download the files


          ⅱ) Set the configuration

 

cd hla-paper

vi haplo_scan_v4.0-hla.py

 

 #PROGRAMS

PROG_BAMTOFASTQ = "./ghaplo_scan"

PROG_BWA = "./bwa"

PROG_FILTEREDBAM = "./allele_count_cpu"

PROG_SAMTOOLS = "./samtools"

PROG_HLASCAN = "./haplo_scan_v4.0"

 

#DATABASE

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

 

          ⅲ) Use script

 

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