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Fig. 1 | BMC Medical Genomics

Fig. 1

From: Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci

Fig. 1

Overview of AA-ALIGNER. Sample genotypes or common variants are used to create a custom reference genome (1). Sequence reads are filtered to remove low quality reads (2) and aligned to the custom reference using GSNAP including alternate alleles (3). Alignments are filtered further to increase alignment quality (4) and used to detect sites of allelic imbalance (5, binomial test) and identify peaks (6). Allelic imbalance is tested at heterozygous sites included in the customized reference genome and at predicted heterozygous sites, identified based on a minimum number of mapped reads containing each of two alleles. If desired, predicted heterozygous sites can be used to update the custom reference and be included in a second alignment repeating steps 3–6

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