I'm trying to find the HLA-B*15:01 variant in my DNA results, prompted from this research paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8142661/#:~:text=HLA%2DB*15%3A01%20is%20strongly%20associated%20with%20asymptomatic,mechanism%20underlying%20early%20viral%20clearance.
I have DNA test results from Dante Labs that contain the following files
"*.bam" "*.bam.bai" "*.cnv.vcf.gz" "*.cnv.vcf.gz.tbi" "*.filtered.indel.vcf.gz" "*.filtered.indel.vcf.gz.tbi" "*.filtered.snp.vcf.gz" "*.filtered.snp.vcf.gz.tbi" "*1_SA_L001_R1_001.fastq.gz" "*SA_L001_R2_001.fastq.gz"
I tried loading this on the Genome Explorer on Sequencing.com, but it couldn't find HLA-B at all, only HLA-A and HLA-C.
Then I tried loading the VCF files in IGV. I was able to filter to Chromosome 6 and HLA-B, which resolved to position
The CNV VCF says no variables found for chr6:31,319,652-31,326,956 The filtered Indel VCF did produce some variants for this position, but I have no clue how to search deeper specifically for HLA-B*15:01. Here is a screenshot:
The filtered SNP VCF produced alot more variants for this position, but again, I don't know how to go deeper than this.
I'm not really sure what to do from here?
I don't have data on what the reference was, so that is unknown to me. I will reach out to Dante Labs about that, is there some sort of standard that is supposed to be used, or is it different for every genome provider?
How do I actually perform the check in IGV assuming the reference did not have it and the VCF did. I also assume this VCF does not have this allele, but I frankly am lost into how to confirm it to the "last mile" through the VCF so to speak, or even just go straight to BAM