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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Rare variant phasing using paired tumor:normal sequence data

Fig. 2

Using duplicated normal samples to identify SCNAs. a The expectation in diploid regions is that that the VAF of heterozygous SNVs will be 0.5; however, due to read sampling error, VAF greater or less than 0.5 is frequently observed. Duplicated normal samples in TCGA can be used as a null model to estimate how often read sampling error resembles an SCNA event by chance. b Distribution of mean segment absolute Δ VAF for 249,471 segments identified from n= 416 duplicated normal samples. Segments were identified using VAF-CBS with a smoothing parameter of 1 Mb. The solid line represents the 95% percentile (absolute VAF = 0.14). QQ plots showing p-values obtained from a Fisher’s exact test on tumor and normal read counts for an example sample c paired tumor:normal tissue, d tumor:normal blood, e normal tissue:normal blood

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