Abstract:Estimating the fraction of cancer cells with individual somatic mutations is central to many analyses in cancer genomics, including characterisation of clonal architecture and timing of mutational events. Estimation of these cancer cell fractions (CCFs) is contingent on unbiased assessment of the fraction of reads supporting variant alleles (VAFs). We demonstrate that VAFs computed by the Illumina Isaac pipeline, used in many large-scale sequencing projects includingThe 100,000 Genomes Project, are biased by t… Show more
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