5 votes
Accepted

What are values of FILTER column of vcf files produced by Mutect2

You haven't told us what commands you ran, so I am assuming you first ran Mutect2 and then FilterMutectCalls. If so, the ...
terdon's user avatar
  • 9,662
3 votes
Accepted

How to introduce point mutations in a protein structure?

PDBFixer and pyMutate are simple, lightweight, free and open-source. Both don't do any optimizing, though, so you may have to run some molecular dynamics afterward to get what would be the right "...
O.Laprevote's user avatar
3 votes

Why can't AlphaFold predict the consequences of point-mutations?

Other have addressed why AlphaFold2 cannot really get the necessary signal from MSA (Multiple Sequence Alignment) and memory to properly model a variant, but I thought I'd add my observations/rants. I ...
Matteo Ferla's user avatar
  • 4,234
1 vote

How to associate point mutations to quantitative protein levels

Yes, you can run an additive model (i.e., B*AA = 2*B*Aa, aa = B*AA - 4*Aa) or a dominance model (B*AA = B*Aa). You can test both of these and see which is a better fit to your data. However, it is ...
BigMistake's user avatar
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

As marcin points out in the comments: by "AphaFold (AF) has not been trained to predict structural consequences of point mutations" it is meant "AF is not able to tell you whether your ...
O.Laprevote's user avatar
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

This answer is from common knowledge rather than specific infield expertise. The question could be more expertly answered by other members. If you really want to pursue this type of calculation, it's ...
M__'s user avatar
  • 11.9k

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