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mourisl / T1K

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.
MIT License
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output interpretation - secondary alleles #29

Closed YuliuG closed 6 months ago

YuliuG commented 6 months ago

Hi, I was using T1K v.1.0.5 for HLA typing. However, from one of the samples (RNA-seq) I got results contains secondary allele. I tried to google it but I still don't quite understand how to interpret it. As I can see, the quality score for secondary allele is also high. Does this mean the patient is expressing more than two alleles? Could it be a sign of potential mutation on HLA alleles? I'd like to hear your thoughts and interpretation on this one. I appreciate it.

HLA-A 2 HLA-A*29:02:01 2338.397334 60 HLA-A*11:01:01 1732.617518 60 HLA-A*11:303;457.673183;60

mourisl commented 6 months ago

These are alleles that pass the abundance threshold but do not optimize the number of overall explained reads. You can disregard these secondary predictions. They are mainly used for debugging and copy number inference.

YuliuG commented 6 months ago

Thank you!