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NCBI-Codeathons / super-minityper

Long Read SVs
MIT License
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PAF/GAF-based SV typing script #4

Open edawson opened 5 years ago

edawson commented 5 years ago

We need a downstream python analysis script that does the following:

Given a GFA and PAF, try to answer the following questions:

  1. Does a given PAF support a given SV (i.e., does a PAF have a mapping to a specific node?)
  2. What is the phasing of the PAF/GFA through the GFA (Trace a PAF through nodes in the graph)
venner commented 5 years ago

Some background reading, looks like GFA defined here: https://github.com/GFA-spec/GFA-spec/blob/master/GFA2.md

And PAF: https://github.com/lh3/miniasm/blob/master/PAF.md

Fu-Yilei commented 5 years ago

https://github.com/dwinter/pafr just found a PAF visualization tool

edawson commented 5 years ago

This requires rGFA + annotation tags mapping from the GFA back to the VCF, which isn't a ton of work but probably needs to be under unit testing in svaha2. We can maybe do this in The Future.