search

RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
113 stars 49 forks source link

Which genes does arcasHLA support? #93

Closed slowkow closed 1 year ago

slowkow commented 1 year ago

IMGTHLA/alignments release 3.49.0 includes:

A,B,C,DMA,DMB,DOA,DOB,DPA1,DPB1,DQA1,DQA2,DQB1,DRA,DRB,E,F,G,HFE,MICA,MICB,TAP1,TAP2

Can we genotype all of these genes with arcasHLA by using the following command?

arcasHLA genotype R1.fq.gz R2.fq.gz -g A,B,C,DMA,DMB,DOA,DOB,DPA1,DPB1,DQA1,DQA2,DQB1,DRA,DRB,E,F,G,HFE,MICA,MICB,TAP1,TAP2

Or are we limited only to these genes?

A,B,C,DPB1,DQB1,DQA1,DRB1
olekskrav commented 1 year ago

Hi Kamil. Thank you for your interest in our tool. The choice of genes is limited to the ones listed in the file dat/info/parameters.json, which are currently as follows:

A,B,C,DMA,DMB,DOA,DOB,DPA1,DPB1,DQA1,DQB1,DRA,DRB1,DRB3,DRB5,E,F,G,H,J,K,L

If you do not supply the -g/--genes argument, all these genes will be considered by default.

We are planning to add the missing genes in a future release. (Similar issues: #60, #56, #38, #15.)