Software For MHC Typing Using Mouse NGS (WES or RNAseq)?

Question

[kilcdincer]

Hello,

I am looking for a tool for typing my mouse WES (Illumina paired-end reads) or RNAseq data for their MHC I alleles. Most of the tools are for HLA typing.

Do you know any tools for my case? Let me know please!

Thanks in advance!

Answer 1

[mourisl]

Do you have the mouse MHC allele sequences? I think the mouse from the strain/breed will be of the same MHC allele, so there is not much need for genotyping them. The IPD-MHC curates rat MHC allele sequences, may be those are helpful? Another source could be from JAX lab to obtain the SNP for different alleles (Where To Download Cds Of Mouse Mhc), and create the allele sequences using procedure like https://github.com/mourisl/T1K/tree/master/vcf_database. Once you have the allele sequences, you can directly run T1K (https://github.com/mourisl/T1K) on it for genotyping. T1K supports both WES and RNA-seq data.