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Fig. 3 | BMC Bioinformatics

Fig. 3

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

Fig. 3

Comparison of phasing methods. Comparison of VAF phasing to read backed, population based, and laboratory phasing methods. a The fraction of germline heterozygous variants phased by HapCUT2 alone, HapCUT2 and phASER, and by HapCUT2, phASER, and VAF in n= 6180 samples. b The fraction of germline variants phased that are unique to each method. c Pairwise discordance between VAF phasing and SHAPEIT for n = 6263 samples as a function of distance and allele frequency. Pairs of variants were binned according to distance between the variants in base pairs and binned according to minimum allele frequency of the variant pair. Colors represent allele frequency bins. Solid lines represent the mean discordance, dotted lines are mean + = 2 s.e.m. d Pairwise discordance between VAF phasing and 10X Genomics phasing for the COLO829 cell line as a function of distance and allele frequency

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