Fig. 3
From: Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls
Characteristics of variant calls in WGA samples. a Individual LOF indel burden vs. individual LOF SNV burden. Color indicates WGA status. b Total number of variant calls plotted by WGA status. c Number of genes with 0 read depth across 16,824 genes. d Fraction of insertions and deletions in n = 5654 WGA-enriched and n = 34,880 non-enriched indels. Shading indicates LOF status. e Size in base pairs of WGA-enriched and non-enriched indels. f Density plot showing distribution of insertion and deletion size for WGA-enriched and non-enriched indels. g Individual burden of LOF indels for all indels, homopolymer + indels, indels 15 base pairs or longer, and other indels. Color indicates WGA status. Indel burden calculated using GATK VQSR TS99 filter