Figure 1
From: A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data
Schematics of CHAT pipeline. Tumor and Normal DNA samples are profiled for allele-specific copy number alterations by SNP arrays and somatic mutations by DNA sequencing. Gray texts and broken arrows (in the upper portion of the figure) indicate input data. CHAT offers two options to partitions the genome: by naturally identified sCNAs or by predefined bins. It then estimates sAGP for each partition (left side). Inference of CCF and timing-phase scenarios relies on sAGP of sCNA, copy number configuration (nb, nt), and SAF of the mutation (right side). CCF and sAGP can be used in a wide range of downstream analyses (bottom).