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jasperlinthorst / reveal

Graph based multi genome aligner
MIT License
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Reference projection in variants #28

Closed fbemm closed 5 years ago

fbemm commented 5 years ago

Hey Jasper,

is there a straight forward way to add the chosen reference (as path) to the GFA generated by reveal rem (as part of reveal align)? Sort a to be able to project variants back to original reference path in the end.

Cheers, Felix

jasperlinthorst commented 5 years ago

Hi Felix, Im not completely sure if I understand your question, but in theory, if you use 'reveal variants' you should with the -r parameter be able to project variants onto any of the paths that are encoded in the graph. If the reference that you use for transform is not in there you should able to add it using 'reveal rem '. The shell script generated by 'reveal align' should do this as well.

However, as decomposing the graph into bubbles depends on having a directed acyclic graph I currently first remove the 'untransformed' paths through the graph (the ones with a *-prefix). This is a bit 'harsh' and I agree it's not ideal, but it mostly fits my needs as I almost always interpret my variants with respect to a single reference.

Is this your problem? Jasper

On Tue, Nov 27, 2018 at 4:27 PM Felix Bemm notifications@github.com wrote:

Hey Jasper,

is there a straight forward way to add the chosen reference (as path) to the GFA generated by reveal rem (as part of reveal align)? Sort a to be able to project variants back to original reference path in the end.

Cheers, Felix

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fbemm commented 5 years ago

Hey Jasper,

I think you got me right. I want to do the same thing. And I was sort a stupid when looking at the file. Everything is there! Would it be possible to restrict the output of reveal variants to multiple references?

Thanks a lot! Felix

fbemm commented 5 years ago

Mh, but that can also be done using a simple grep ;)