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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.
Suggested approach
No response
Considered alternatives
No response
Deviation
No response
System requirements assessed
Yes, I have reviewed the system requirements
Requirements affected by this story
No response
Risk assessment needed
Needed
Not needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response
The text was updated successfully, but these errors were encountered:
Need
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.
Suggested approach
No response
Considered alternatives
No response
Deviation
No response
System requirements assessed
Requirements affected by this story
No response
Risk assessment needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response
The text was updated successfully, but these errors were encountered: