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RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
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Typing of DPA1 #38

Closed tinyheero closed 4 years ago

tinyheero commented 4 years ago

Hi there,

Thanks for this tool. Is it possible to use arcasHLA to type DPA1? The documentation contains output for DPB1, but ti doesn't seem to be output for the alpha chain.

Kind regards,

Fong

IoanFilip2 commented 4 years ago

Dear Fong, thank you for your interest in arcasHLA. The documentation serves an illustrative purpose. When the user does not supply a list of genes to genotype as a parameter, the default option returns genotyping for all the class I, class II and even pseudogenes. In particular, DPA1 is genotyped as well. This is the full list of genes under the default option: ['A', 'B', 'C', 'DMA', 'DMB', 'DOA', 'DOB', 'DPA1', 'DPB1', 'DQA1', 'DQB1', 'DRA', 'DRB1', 'DRB3', 'DRB5', 'E', 'F', 'G', 'H', 'J', 'K', 'L'].