HLA alignment, approximation and frequencies

Question

[oumo]

Hello, I have tried aligning this fastq file (long reads from ONT sequencing) with minimap2. I came up with a sam file, converted to bam file, sorted and indexed it. I want to come up with HLA types and frequencies, but stuck here.... It seems some key steps enter code here

$ minimap2 -ax map-ont A_gen.fasta HLAs.fastq > HLA.sam
$ samtools view -Sb -o HLA.bam HLA.sam
$ ls
$ samtools sort -o HLA-sorted.bam HLA.bam
$ samtools index HLA-sorted.bam

[marco.barr]

Hi, to proceed with HLA typing and determining frequencies, you can use specialized tools designed for this purpose. Here are a few options: 1) OptiType ; 2) SpecHLA.

They works with both short and long reads and allow you to extract HLA-specific reads and then obtain typing. I'm not an expert in downstream analysis of this type but just do a search and you'll find something about it. I hope I have been of help to you.

Regards,

Marco

[oumo]

Thank you Let me check out these specialized tools