SuperFreq: Integrated mutation detection and clonal tracking in cancer
Fig 3
Comparison of somatic CNA calls for 304 TCGA participants across 33 cancer types.
(A) Distribution across participants of the fraction of the genome that agrees with ASCAT. Agreement is defined as LFC and BAF within 0.145 and 0.05 respectively, roughly corresponding to a 20% clonality gain or loss. The blue violins show only participants with a ploidy estimate within 0.2 of ASCAT. (B) SuperFreq recall of somatic CNAs in diluted and sliced samples analysed without the matched normal, with the original cancer-normal analysis used as truth. Each bin is based on at least 100 copy number segments. (C) Comparison of ploidy estimates between ASCAT, ABSOLUTE and SuperFreq, coloured by number of somatic clones called by SuperFreq. Samples were excluded if no somatic clone was called. (D) Recall of gain, loss and CNN-LOH binned by size of the segment, limited to participants where the ploidy agrees within 0.2 between the methods.