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andersen-lab / Freyja

Depth-weighted De-Mixing
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Some problem about the UshER barcodes output #210

Closed Bin-Ma closed 3 months ago

Bin-Ma commented 4 months ago

Hi @tomkinsc,

I have some questions about the UshER barcodes output in "https://github.com/andersen-lab/Freyja/tree/main/freyja/data".

  1. Is this file generated from UshER's VCF files in "http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/"?
  2. Is there any way or script to convert the VCF format to CSV format?

Looking forward to your reply!

Bin

joshuailevy commented 3 months ago

Hi!

  1. Yes it is.
  2. It should already be in CSV format: https://github.com/andersen-lab/Freyja/blob/main/freyja/data/usher_barcodes.csv

Best, Josh