Confusion about the optional zero step

[Yang Shi]

Hi, I am using optitype for HLA typing, thanks for developing such a wonderful tool!
I firstly use razers3 and samtools to extract the reads mapped to hla genes(zero step), and then use OptiTypePipeline.py for downstream analysis. I wondered that if I directly run OptiTypePipeline.py on initial fastq files without step0, will it take more time than step0 + OptiTypePipeline.py? If not, what is the significance of step0?
Thank you very much!

[andras86]

Hi! It is totally optional. The smaller fastq files are only really useful if you ever re-run OptiType on the same sample, with a different beta setting or discordant read-end policy or something. It shouldn't take much more time though. Anyway, you can safely leave out step 0.

[Yang Shi]

Got it! Thank you!