Fig. 1
From: Low-cost and clinically applicable copy number profiling using repeat DNA
Comparison of conliga method with ASCAT, QDNAseq and CNVkit. a Total copy number (TCN) profile determined by ASCAT using HC WGS data for sample OAC2, showing all copy number segments. b RCN profile determined by QDNAseq using LC WGS data for sample OAC2, showing all 15 Kbp bins. c TCN profile determined by ASCAT from HC WGS data, d RCN profile determined by CNVkit, e RCN profile determined by conliga, all (c-e) showing copy number calls at the intersection of ASCAT’s called regions and FAST-SeqS loci for sample OAC2. f Comparison of log2 RCN calls from 11 samples between QDNAseq and ASCAT (top), CNVkit and ASCAT (middle) and conliga and ASCAT (bottom). rs represents the Spearman’s rank correlation coefficient. All RCN calls at the intersection of ASCAT’s called regions, QDNAseq 15Kb bins and FAST-SeqS loci in all 11 OAC samples are shown as points. g Distribution of differences between ASCAT RCN calls and QDNAseq RCN estimates for 11 OAC samples (top), ASCAT RCN calls and CNVkit RCN estimates for 11 OAC samples (middle) and ASCAT RCN calls and conliga RCN estimates for 11 OAC samples (bottom). h Comparison of performance at gene-level resolution between ASCAT and QDNAseq for 36 selected genes (top), ASCAT and CNVkit (middle) and ASCAT and conliga (bottom). The values represent the weighted mean of RCN calls at each gene for each of the 11 OAC samples (Methods)