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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Defining personal genomes on a variation graph #40

Closed inti closed 8 years ago

inti commented 9 years ago

Hi, For some analyses, like Allelic Specific Expression, one wants to have a personal version of the reference. That is the reference modified to represent the known sequence of a individual. It seems this would be trivial with variation graphs if one has a set of variants for which a individual is hom/het. Question: is it possible to align the reads against a subset of the paths of the graph? like define a subset of the graph removing paths for alleles not present on a personal genome (it is hom at the site) and keeping only paths for het sites? Thanks in advance

ekg commented 9 years ago

@inti I think this should be possible by annotating paths in the graph. These paths can be used to project alignments (vg surject) against the graph against a particular path. This subgraph could be a personal genome. Does this make sense?

inti commented 9 years ago

Yes, it does make sense. I just have not got chance to try it. I will have a chance soonish. Cheers, Inti

On Jul 13, 2015, at 08:38, Erik Garrison notifications@github.com wrote:

@inti https://github.com/inti I think this should be possible by annotating paths in the graph. These paths can be used to project alignments (vg surject) against the graph against a particular path. This subgraph could be a personal genome. Does this make sense?

— Reply to this email directly or view it on GitHub https://github.com/ekg/vg/issues/40#issuecomment-120898605.

adamnovak commented 8 years ago

I'm going to close this because, while it's a cool project, it's not really a vg bug.

edawson commented 8 years ago

Hey @inti , if you've tried it out let us know - we'd like to hear a success story if you have one, and you can catch us on gitter if for some reason things didn't work!

inti commented 8 years ago

Thanks. I will try to get around to test it and I will let you know. Cheers, Inti

On Sep 21, 2016, at 05:03, Eric T. Dawson notifications@github.com wrote:

Hey @inti https://github.com/inti , if you've tried it out let us know - we'd like to hear a success story if you have one, and you can catch us on gitter https://gitter.im/vgteam/vg if for some reason things didn't work!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/40#issuecomment-248540103, or mute the thread https://github.com/notifications/unsubscribe-auth/AAXApQmmcH2CbqjXi23Z-MP4uCOdhcgHks5qsOTYgaJpZM4E4bA1.