Fig. 6: Comparison of the tumor purity and ploidy estimates computed using different SAVANA modes and ONT WGS data against PURPLE and Illumina WGS data.
a, Tumor purity estimates. b, Tumor ploidy estimates. Panels labelled as ‘SAVANA-paired germline SNPs’ show results for matched tumor-normal pair analysis using matched normal germline SNPs for purity estimation. Panels labelled as ‘SAVANA-paired 1000 G SNPs’ show results for matched tumor-normal pair analysis using the 1000 Genome Project population SNPs with allele fractions >0.25 and allele fractions <0.75. Panels labelled as ‘The SAVANA tumor-only 1000 G SNPs’ show results for analysis using the 1000 Genome Project population SNPs with allele fractions >0.25 and allele fractions <0.75. For this analysis, we only considered the 44 tumors with region-matched nanopore and Illumina WGS data. ***P < 0.0001. The P values for tumor purity comparisons shown in a were P < 2.2 × 10−16, P = 3 × 10−16, P < 2.2 × 10−16, P < 2.2 × 10−16, P = 1.1 × 10−13 and P = 1.5 × 10−14, respectively. The P values for tumor ploidy comparisons depicted in b were P < 2.2 × 10−16, P < 2.2 × 10−16, P = 2.6 × 10−16, P < 2.2 × 10−16, P = 1.1 × 10−13 and P < = 1.9 × 10−12, respectively (reading from top to bottom, left to right).
