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VAF threshold in tumor only mode #39

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flokraft85 opened this issue Oct 2, 2024 · 0 comments
Open

VAF threshold in tumor only mode #39

flokraft85 opened this issue Oct 2, 2024 · 0 comments
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@flokraft85
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Ask away!

Hi,
I would like to ask, if there is a VAF threshold in the tumor only mode. We currently analyze tumor sample in parallel with exome sequencing (~130x) and nanopore sequencing (95x) and compare the results. Unfortunately some of the pathogenic variants in the tumor are missing the wf-somatic-variation VCF, although there are clearly visible when checking the data in IGV.
The missing variants show a low VAF (0.15 and 0.05) and that why I wonder, if there is maybe a threshold for the VAF.
Thanks in advance!
Florian
@flokraft85 flokraft85 added the question Further information is requested label Oct 2, 2024
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