HLA allele from RNA and DNA-seq

Question

[Teresa]

Hi everyone,

Can you please suggest me some software for HLA imputation from DNA and RNA-seq.

Thanks

Answer 1

[Charles Warden]

You might want to check out this post (I think most tools are designed with DNA-Seq in mind, but they might also work with RNA-Seq): Software For Hla Typing Using Ngs?

[Teresa]

Thanks for your kind reply

Answer 2

[Alvaro Sebastian]

Check this article: Bai, Y., Ni, M., Cooper, B., Wei, Y. & Fury, W. Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. BMC Genomics 15, 325 (2014).

They describe their algorithm PHLAT (in my opinion, overrated), but they mention other available tools: HLAminer, HLAforest, seq2HLA. Check the latest versions of these tools.

Good luck.