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 ...
- 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 "...
- 483
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 ...
- 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 ...
- 513
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 ...
- 483
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__♦
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