Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper
Fig 4
WGS Genotyping using FlexTyper.
A) FlexTyper read count compared to the total coverage from BAM file over SNP sites represented on the CytoScanHD microarray. B) Histogram showing the delta, (Δ = FlexTyper—BamCoverage), in read count for both the alternate (red) and reference (blue) alleles. C) Histogram of the same delta as B) but with an extended axis from 100–2000, showing the frequency of over-counting for sites using FlexTyper. D) Scatter plot showing the delta (Δ = FlexTyper—BamCoverage) on the y-axis, plotted across chromosome 1 on the x-axis. E) Principal component analysis showing projection of FlexTyper-derived SNP genotypes from nine individuals of Asian (green), African (red) and European (purple) ancestry. Squares denote FlexTyper genotypes, points denote existing data from the 1000 Genomes project provided by Peddy. F) Sex-typing for these Polaris samples showing the ratio of heterozygous to homozygous sites on the X chromosome (y-axis) for individuals for the defined sexes as male (right) and female (left). Each individual is labeled as green (correctly sex-labeled) or red (incorrectly labeled).