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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Merge GBWT-mpmap into master #1354

Closed adamnovak closed 6 years ago

ekg commented 6 years ago

Is there a function in GBWT that allows checking the frequency of a given haplotype? If so then there is a five line chunk of code that we can add to the mapper to provide haplotype panel awareness to its scores.

adamnovak commented 6 years ago

I've been working on that for the normal mapper, actually. It's turned out to be a little more than 5 lines, because I want to adjust the scores of all the mapping locations of the read, and because some mapping locations can't be correctly scored yet. But it's in there right now if you provide a GBWT file that was generated along with your xg.

On Thu, Jan 11, 2018 at 9:47 AM, Erik Garrison notifications@github.com wrote:

Is there a function in GBWT that allows checking the frequency of a given haplotype? If so then there is a five line chunk of code that we can add to the mapper to provide haplotype panel awareness to its scores.

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