Figure 4: Distribution of tumour LOD scores in cfDNA sequencing data.
From: Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates
For each sample, all candidate mutation calls generated by muTect version 1.1.4 were divided into subgroups based on the type of mutation or the filtering step at which they were removed, as indicated in the legend. The stripcharts showing the tumour LOD scores for each subgroup of mutations were overlaid with the boxplot demonstrating the distribution of tumour LOD scores for all mutation calls kept by muTect within each sample, prior to downstream filtering. The central rectangle spans the first to the third quartile (IQR), and segment inside the rectangle shows the median tumour LOD score for each sample. Sample-specific thresholds for calling likely somatic mutations (−) were determined as the tumour LOD score corresponding to the modified Z-score of 20 (that is, 20 MADs above the median). Unfiltered annotated data for all samples are available as Supplementary Data 2. Custom Rscripts (in R version 3.2.2) for filtering and plotting LOD score distribution data are available at www.github.com/pughlab/lb-seq.
