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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Finding a suitable library size to call variants in RNA-Seq

Fig. 2

Sensitivity using the TCGA-LAML truth sets. a 2D Density plots of the RNA VAF (x-axis) against the total depth on a logarithmic scale (y-axis) of the SNVs in TCGA-LAML validated sets of variants: Set1 (all SNVs after removing intronic and intergenic variants) on the left and Set2 (SNVS on recurrently mutated AML genes) on the right. b Violin plots of the log2RPKM of the genes with variants detected in Set1 and Set2. The gene expression distributions are provided for the TCGA-LAML and the Leucegene libraries using the initial samples, before downsampling. c Sensitivity in recovering SNVs from the TCGA-LAML cohort in the initial and downsampled libraries using a combination of the two truth sets, callers and filtering strategies

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