Additional file 1.

Supplementary material. This file contains Figures S1, S2, S3 and S4, and Tables S1, S2, S3, S4 and S5. Figure S1 presents a schematic of our pre-processing pipeline. Figure S2 presents the length distribution of our CNV calls. Figure S3 presents the cumulative length distribution of cnvHiTSeq calls that were validated with array-CGH data. Figure S4 presents a heatmap of the genotyping concordance between cnvHiTSeq and a benchmark dataset. Table S1 presents the array-CGH validation results. Table S2 describes the computational requirements of our pipeline. Table S3 presents a comparison of our deletion calls with those of Genome STRiP for sample NA12878. Table S4 presents a comparison of our Mendelian inconsistency results for different criteria. Table S5 presents a comparison of the sensitivity of various methods on low-coverage samples.

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Bellos et al. Genome Biology 2012 13:R120   doi:10.1186/gb-2012-13-12-r120