Supplementary Figure 2: Benchmark of TL and TL ratio across centers and sequencing methods.

(a) Boxplots showing log(TL) across centers and sequencing methods. Each point indicates the median for a single cancer type. BI, Broad Institute sequencing center; BCM, Baylor College of Medicine sequencing center; WUGSC, Washington University sequencing center; HMS-RK, low pass sequencing. (b) Boxplots showing the log(Tumor TL/Normal TL) ratio across centers and sequencing methods. Each point indicates the median for a single cancer type. (c) Comparison of n = 3,883 log(TL) replicates. Sequencing center was kept constant for comparison across sequencing method and was variable for comparison within sequencing method. Replicate pairs that did not follow these criteria were dropped. (c) Boxplots showing the log(Tumor TL/Normal TL) ratio across centers and sequencing methods. Each point indicates the median for a single cancer type. (d) Comparison of n = 1,861 T/N TL ratio replicates. Sequencing center was kept constant for comparison across sequencing method and was variable for comparison within sequencing method. Replicate pairs that did not follow these criteria were dropped.