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[User Story] Tumor in normal contamination filter in VarDict #1494

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mathiasbio opened this issue Oct 22, 2024 · 0 comments · Fixed by #1475
Closed
3 tasks

[User Story] Tumor in normal contamination filter in VarDict #1494

mathiasbio opened this issue Oct 22, 2024 · 0 comments · Fixed by #1475
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@mathiasbio
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As a clinician I want to avoid needing to interpret artefacts, currently the VarDict filter for presence of the variant in normal is based strictly on whether the variant in the tumor is observed in roughly above 5% in the normal. (See: #1256) This is a strict filter for variants with high frequency in the tumor, allowing very little tumor in normal contamination, while being very relaxed for low frequency variants which are commonly artefacts. By applying a relative fraction as was done for TNscope previously (see: #1335) we can remove variants which are about equally represented in tumor and normal and which are commonly artefacts.

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@mathiasbio mathiasbio added the User-Story A User-Story describing new functionality label Oct 22, 2024
@github-project-automation github-project-automation bot moved this to Todo in BALSAMIC Oct 22, 2024
@mathiasbio mathiasbio moved this from Todo to Completed in BALSAMIC Oct 22, 2024
@mathiasbio mathiasbio added this to the Release 16 milestone Oct 22, 2024
@mathiasbio mathiasbio linked a pull request Oct 22, 2024 that will close this issue
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