Fast imputation of variants for 4x WGS?

Question

[14134125465346445]

Are there any tools to impute variants from a 4x WGS caucasian genome that won't take 32 CPU years to compute, like they did for the 1000G 4x dataset?

Is there an imputation algorithm that could update one sample rapidly conditional on 1000 pre-computed samples?

Answer 1

[Brian Bushnell]

I'm not sure what you are asking, exactly. It sounds like you are asking this:

I have 4x coverage of a person. How can I find out what variants he has from the human reference, in under 32 CPU-years?

If that's correct, well, you can use any modern software; the more difficult question would be how to spend 32 CPU-years calling variants on 4x human data. But then it also sounds like you want to maintain some kind of dynamic database, which makes little sense in the context of your question. So, what exactly are you trying to do?