Fig. 2 | Nature Communications

Fig. 2

From: A reference haplotype panel for genome-wide imputation of short tandem repeats

Fig. 2

Creating a reference SNP-STR haplotype panel. a Schematic of phasing pipeline in the SSC cohort. To create the phased panel, STR genotypes were placed onto phased SNP haplotypes using Beagle. Any missing STR genotypes were imputed. The resulting panel was then used for downstream imputation from orthogonal SNP genotypes. Blue and red denote phased and unphased variants, respectively. Positions in gray are homozygous. b Concordance of imputed STR genotypes vs. expected heterozygosity. Blue denotes observed per-locus values, green denotes values expected under a random model and orange denotes values expected under a naive model. Solid lines give median values for each bin and filled areas span the 25th to 75th percentile of values in each bin. x-axis values were binned by 0.1. Upper gray plot gives the distribution of expected heterozygosity values in our panel. Concordance values are based on the leave-one-out analysis in the SSC cohort. c Per-locus imputation concordance in SSC vs. 1000 Genomes cohorts. Color scale gives the log10 number of STRs represented in each bin. Concordance values are based on the subset of samples from the 1000 Genomes deep WGS cohort with European ancestry. d Per-locus imputation concordance using HipSTR vs. capillary electrophoresis genotypes. Each dot represents one STR. The x-axis and y-axis give imputation concordance using capillary electrophoresis or HipSTR genotypes as a ground truth, respectively. Concordance was measured in separate sets of 1000 Genomes European samples for each technology. e Concordance of imputed vs. 10X STR genotypes in NA12878 stratified by concordance in SSC. STRs were binned by concordance value based on the leave-one-out analysis. Concordance in NA12878 was measured across all STRs in each bin. Dots give mean values for each bin and lines denote ±1 s.d. In all cases leave-one-out refers to analyses performed in the SSC cohort

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