Fig. 2

Copy-number segments identified by HATCHet2, HATCHet [30], and Battenberg [23] in prostate cancer. A (Top) Lengths of segments identified by the three methods from 10 prostate cancers from Gundem et al., 2015 [42]. Dotted gray lines indicate 1 kilobase and 1 megabase. (Bottom) Numbers of segments inferred by each method on each prostate cancer patient. B Number of segments identified by each method for each patient (row) within 1 megabase of 41 genes (columns) from The Cancer Genome Atlas prostate cancer publication [72]. C Copy-number segments identified by HATCHet2 near the TP53 locus on chromosome 17 in one sample from patient A12. (Two other samples from this patient are shown in Additional file 1: Fig. S3.) Each point is a small genomic region that contains exactly one SNP with indicated read-depth ratio (RDR) and B-allele frequency (BAF) and is colored by the assigned copy-number state for the corresponding method. Black bars indicate the expected RDR and BAF of each segment according to the copy-number states and clone proportions assigned by the corresponding method. Gene location is indicated by vertical purple bar. Full copy-number state legends for panels C–F are reported in Additional file 1: Fig. S5. D Copy-number segments identified by HATCHet near TP53 for the same sample as panel C (Battenberg results for this patient are shown in Additional file 1: Fig. S3). E Copy-number segments identified by HATCHet2 and F Battenberg near the CANT1 locus on chromosome 17 in two samples from patient A10 (two other samples from this patient are shown in Additional file 1: Fig. S4)