Find related samples based on a list of variants

Question

[igor]

Is there a tool that can take a list of mutations (in a VCF file or just a list of positions) from multiple samples and then cluster the samples based on how closely related they are?

This may not be very complex, but as far as I know, it would involve a few steps and I don't want to reinvent the wheel, especially if I may not do in the most appropriate way. I assume someone has already automated the process. Maybe even with really nice graphs as an output.

[Pierre Lindenbaum]

"Yes, this is not very complex" , AKA "I have discovered a truly marvellous proof of this, which this margin is too narrow to contain." :-)

[igor]

I guess I meant "this may not be very complex". The reason for my assumption is there does not seem to be an available solution, which usually means it's either trivial or extremely difficult (which is definitely not the case here).

Answer 1

[harold.smith.tarheel]

Sounds like a phylogenetic tree would work. SNPhylo (reference here) can take VCFs as input and create distance tree graphs.

[igor]

Sounds very promising. It looks like it needs a single multi-sample VCF, though. Or can it take multiple single-sample VCFs?