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hanfang / Topsorter

Graphical assessment of structrial variants using 10x genomics data
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Current priorities #2

Open hanfang opened 7 years ago

hanfang commented 7 years ago

Done:

  1. Finish modules for importing barcode coverage
  2. Translocation. One chromosome at a time. Evaluate like deletions but different schemes.
  3. Prepare survivor calls in vcf format.
  4. Output: vcf format. Add a tag: boolean. Temp tags: barcode counts.
  5. Currently supports manta format, will need to support lumpy format later.
  6. Length checking for chromosome ends.
  7. Better graph visualization.
  8. Graph building optimization to deal with overlapping variants.
  9. Draw illustration figure with edge weights

To-do:

  1. Simulate 10x data and benchmark
  2. Inspect on IGV about some variants and the barcodes
fritzsedlazeck commented 7 years ago

Done with 3

hanfang commented 7 years ago

Thanks @fritzsedlazeck. Item 2 is done. The placeholder for item 4 is also there.

Regarding item 1, we need to deal with the things from this issue. How long will it take @srividya22 to finish this?

hanfang commented 7 years ago

@srividya22 is working on item 1. item 4 is also done.

hanfang commented 7 years ago

Item 7 is done. Currently working on 8.

hanfang commented 7 years ago

Item 6 and 8 are done

hanfang commented 7 years ago

Item 5 11 is done