Variant allele frequency with copy number
the variant allele frequency(VAF) related to time-series, e.g. higher VAF related to early mutation, lower VAF related late occurred mutation.
However, if the copy number amplification with late occurred mutation, this VAF might high if mutation allele- amplified or low if wild-type allele amplified.
is there any tools to handling this kind of problem? to calculate corrected VAF?
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