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
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