search

DaehwanKimLab / hisat-genotype

GNU General Public License v3.0
23 stars 15 forks source link

Would hisat-genotype work with Panel sequencing ? #35

Closed npatel-ah closed 3 years ago

npatel-ah commented 3 years ago

Dear Author,

Can the hisat-genotype be used for small gene panels or WES data for HLA typing ?

I was following the reference manual for the hisat-genotype, which has no mention regarding WES or small panel. The tool utilizes HISAT2 for graph representation and alignment. So if I understood the algorithm correctly from the recent paper https://pubmed.ncbi.nlm.nih.gov/31375807/ , the first step is to create the linear graph, which will be robust for WGS but unsure how it will work with WES and especially with Panel sequencing.

Best, Nihir

chbe-helix commented 3 years ago

Hi Nihir,

You should have no issues running hisat-genotype for panel or exome sequencing. You may only need to restrict the scope of the program to the regions of interest. For example, if you sequence the HLA-A, HLA-B, and HLA-DRB1 regions only you'd want to run hisat-genotype with --base hla --locus-list A,B,DRB1 options. If you encounter any issues let me know.

Thanks, Chris

npatel-ah commented 3 years ago

Really appreciate your quick response and suggestions