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dcgerard / updog

Flexible Genotyping of Polyploids using Next Generation Sequencing Data
https://dcgerard.github.io/updog/
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How to get the VCF file #14

Closed yudizhangzyd closed 3 years ago

yudizhangzyd commented 3 years ago

Hi there,

I was trying to use this tool, but my question is: is your tool a reference free method? If yes, then how to get such VCF files, thanks.

Yudi

yudizhangzyd commented 3 years ago

Plus, does it work for just one individual? Thanks.

dcgerard commented 3 years ago

Hey @yudizhangzyd, thanks for trying out updog!

You need to use some other variant caller to come up with the VCF file. So, you can try out GATK, FreeBayes, or TASSEL. A reference free approach is written up here. You might find this document helpful.

Best, David

dcgerard commented 3 years ago

For your second question, it works for multiple individuals.

Best, David

yudizhangzyd commented 3 years ago

Thanks David!

dcgerard commented 3 years ago

Hey @yudizhangzyd, I've heard folks say not to use UNEAK anymore. But I have seen others use NGSEP, and their paper has some nice references which might be useful: https://doi.org/10.1101/2020.11.28.402131