Fig. 4
From: Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping
Examples of discordant calls caused by allele imbalance. (a) Discordant ABCB1 diplotype call in HG01572. rs2032582 was incorrectly called as homozygous alternate (TT) in long-read data, while short-read data supported a heterozygous genotype (TC). The C allele is present in the long reads, but its coverage is too low to meet the variant calling threshold. (b) Discordant CYP4F2 call in sample NA18966. TAS-LRS wrongly called the rs2108622 as homozygous alternate, whereas other platforms including GeT-RM, microarray (GSAv3), and short-read pipelines showed the diplotype as *1/*3. IGV plots show insufficient coverage of haplotype 1 for this specific sample.
