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tjblaette / getitd

Software for FLT3-ITD detection and MRD monitoring assay
MIT License
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Question of getITD output column information & filtering #15

Open sungyoonkimb opened 1 year ago

sungyoonkimb commented 1 year ago

Hi, I'm writing to ask about the getITD tool.

I'm curious about the exact meaning of some terms in getITD.

  1. I'm wondering exactly what 'copy' means in the -min_read_copies option. My current guess is either forward/reverse copies of the read or two copies of the position when mapping.
  2. I'm curious about the meaning of 'sense' in output column and the meaning of {1,-1} respectively. Does it indicate which strand was detected?
  3. I'm curious if the variants detected by getITD are categorized by insertion and by what criteria in the itd output file.
  4. finally, I know that the filtering of the output file of getITD goes as follows: is-same -> is-similar -> is-close -> is-same-trailing -> hc to generate the file, but I would like to know what is checked in each step.

Thanks for developing such a good tool.