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kage-genotyper / kage

Alignment-free genotyper for SNPs and short indels, implemented in Python.
GNU General Public License v3.0
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looking for some suggestions #8

Open unavailable-2374 opened 6 months ago

unavailable-2374 commented 6 months ago

If I want to genotype SNPs, InDels and SVs, should I create two indexs, one for SNPs and InDels, and another for SVs, then run kage genotype twice?

ivargr commented 6 months ago

Hi!

I think you in most cases should be fine just creating one index for all cases. The only downside is that KAGE will ignore some SNPs/indels that are covered by SV-deletions. In many cases this might not be a problem or a big deal, but if you want to ensure this does not happen, it is better to create a separate index only for genotyping SNPs/indels.

Let me know if you have any other questions or if anything was unclear.

unavailable-2374 commented 6 months ago

Thank you, you're very kind!

I hope your work gets published in a prestigious journal 🫶

I have a minor question about using '-glimpse.' When I reviewed the 'glimpse_wrapper.py' script, I noticed it uses glimpse version V1.1.1, though the latest version is V2.0.0. Is there a specific reason for choosing V1.1.1 over V2.0.0😬

ivargr commented 6 months ago

Thanks! :)

Regarding GLIMPSE, the reason is simply that according to the GLIMPSE documentation, the first version seemed more appropriate since GLIMPSE 2 seems to be designed mainly for low coverage data. We havn't really tried GLIMPSE 2 since GLIMPSE 1 turned out to work well, but it might be that GLIMPSE 2 would also work fine.