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This article will explain in detail how to use HLAscan for HLA typing, the content of the article is of high quality, so the editor will share it for you as a reference. I hope you will have a certain understanding of the relevant knowledge after reading this article.

HLAScan is a HLA typing tool developed by a Korean research team, which can process WGS, WES and target area capture and sequence data, compare reads with reads in IMGT/HLA database, and then determine the genotype information of HLA.

The software development team used the test data to evaluate the typing effect of the following software

You can see that HLAscan can provide reliable 2-bit and 4-bit typing results. The link to the official website is as follows

Http://www.genomekorea.com/display/tools/HLAscan

The latest version is hlascan_v2, and the installation process is as follows

Unzip hla_scan_r_v2.1.2.zipunzip data-set.zip

In addition to the software installation package, the official also provides a test data set, which can be used by downloading and decompressing directly. The basic usage is as follows

Hla_scan_r_v2.1.2-b NA12155.chr6.bam-d HLA-ALL.IMGT-v 38

The-b parameter specifies the input bam file,-d specifies the name of the database, which is included with the software, and-v specifies the genome version hg38.

The software defaults to HLA-A genotyping. In addition to this gene, it also supports the typing of the following genes.

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

The software also supports providing input sequences in fastq format directly. For specific usage, please refer to the description on the official website.

The following log information will be displayed during the run

= HLAscan v2.1Report created2018. 7. 23. 11:25:32===HLA gene: HLA-A# of considered types: 3182-HLA-Types-[Type 1] 01 EX3_3.29348_45 EX2_3.75926_100 EX4_24.0471_100 EX5_35.1966_100 11N EX3_3.29348_45 EX2_3.75926_100 EX4_24.0471_100 EX5_35.1966_100 [Type 2] 01purl 11N EX3_3.29348_45 EX2_3.75926_100 EX4_24.0471_100 EX5_35.1966_100

It can be seen that for HLA-A gene, the result of genotyping is HLA-A*01:11N.

On how to use HLAscan for HLA typing is shared here, I hope the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.

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