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NCBI-Codeathons / super-minityper

Long Read SVs
MIT License
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Build Genome in a Bottle SV Graph in GFA #3

Closed edawson closed 4 years ago

edawson commented 4 years ago

We need to build the GIAB SV graph in a minigraph-compatible GFA format (https://github.com/lh3/minigraph)

  1. Download SV calls
  2. Harmonize them in their VCF format.
  3. GRCh37 + sv calls -> GFA using svaha2 (https://github.com/edawson/svaha2)
edawson commented 4 years ago

So this got built, but minigraph doesn't like my input. Can someone help me peek through the GFA file + the GFA specs to see what I did wrong? I think it's probably an easy fix.

Fu-Yilei commented 4 years ago

GFA+fa/fq -> minigraph -> GAF, right? I think I just did several simulations with the sample data, guess I can help. I got your GFA file - hg002.sv.gfa - form DNA nexus, but I am not sure which read you are using?