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Missing position #388

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alantsangmb opened this issue Aug 20, 2024 · 1 comment
Open

Missing position #388

alantsangmb opened this issue Aug 20, 2024 · 1 comment

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@alantsangmb
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alantsangmb commented Aug 20, 2024

Hi, I have asked the same question in issue#164. However, I am afraid that question was missed, so I am opening another issue. I apologize for the repeated question. However, I really want to understand how the results are being flagged as missed. For the missing position part, am I right that TBProfiler would report the regions that lack sufficient coverage for the mutations listed in the tbdb mutation list, including those with uncertain and "not associated w R" confidence?

Thank you.

@jodyphelan
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Hi @alantsangmb

Apologies for the delay in getting back to you. There has been a bit of inconsistency between versions but in the latest version the missing positions section will only contains variants that are Assoc w R or Assoc w R - Interim. All positions are internally extracted but this caused some issues where the output json files were huge for samples with low coverage.

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