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Figure 1 | BMC Bioinformatics

Figure 1

From: KRLMM: an adaptive genotype calling method for common and low frequency variants

Figure 1

Signal characteristics. Plots showing typical signal for common SNPs (top row) and SNPs with lower MAF (bottom row). Panels B and C show examples of SNPs with asymmetric signal which is shifted up or down towards the heterozygous cluster. The x-axis displays average signal (S= 1 2 [ log 2 X ∗ + log 2 Y ∗ ]) and the y-axis the log-ratio (M = log2X∗- log2Y∗). The allelic signals (X∗, Y∗) have been quantile normalized as described in the Methods. The presence of 3 (A-D), 2 (E) or 1 (F) distinct cluster motivates our approach to genotype calling that uses the data available for each SNP to predict the number of clusters prior to clustering. These examples are from the Omni2.5-Quad platform.

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