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. 2016 Dec 20;5:2644. Originally published 2016 Nov 7. [Version 2] doi: 10.12688/f1000research.9912.2

Figure 4. Haplotype Caller small variant results.

Figure 4.

A: Density of common variants across the genome (MAF>0.05 (Variants from the in-house reference line are included but account for less than 3,686 of the 1,825,917 common variants plotted (<0.2%). B: Allele frequency distribution by variant type. *MAF values were calculated from the count of heterozygous calls, and so for multi-allelic variants, the MAF is derived from the combined count of both alternate alleles. C: Genotype counts per individual genotyped. Data generated using GATK/3.4 VariantEvaluation function. Data and R code for this figure are located at https://doi.org/10.5281/zenodo.159282.