SuperFreq: Integrated mutation detection and clonal tracking in cancer
Fig 1
The input is aligned BAM files from the samples under study, and at least 2 reference normals (5–10 recommended, see methods), as well as liberal variant calls. SuperFreq filters the preliminary SNVs for artefacts using quality scores in the BAM file, and through comparison to the reference normals. Somatic SNVs are called from the remaining variants, while heterozygous germline SNPs are identified for CNA calling. CNAs are identified based on differences in coverage and detecting shifts in allele frequency at heterozygous germline SNPs. Finally, somatic SNVs and CNAs are analysed across samples to designate and track clones.