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DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs
http://dx.doi.org/10.1038/ng.3964
MIT License
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What does that mean？（FT=FAIL1/FAIL2/FAIL3！） #106

Open yinmou21 opened 2 years ago

yinmou21 commented 2 years ago

Hi，

Thank you so much for developing such a nice program.

The output of GraphTyper2 contains something: FT=FAIL1 or FAIL2 or FAIL3！

image

What does that mean, please?

Thank you very much for your answer!

hannespetur commented 1 year ago

Hi. It is different failure levels, higher lever means less confident call. Basically it looks at what the other genotype models are calling and gives FT=PASS if all the models are in high agreement, FAIL1 means there is some slight disagreement, and so on.

Sreelekshmi-291 commented 1 day ago

Hi @hannespetur Can you clarify what you meant by "other genotype models"? Are you talking about models like AGGREGATED and BREAKPOINT here? Can you please explain how many models there are and on what basis they tag the SV entries as PASS or FAIL?

I really appreciate any help you can provide.