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Figure 3 | Genome Medicine

Figure 3

From: Choice of transcripts and software has a large effect on variant annotation

Figure 3

ENSEMBL -normalised heatmap of annotation comparisons. This heatmap shows scaled numbers of variants (log10 transformation with offset of 1 applied) for all different combinations of ANNOVAR categories of annotations when using the ENSEMBL transcript set (columns) and REFSEQ transcript set (rows). Values are Z-scaled (mean-centred, divided by standard deviation) by column (each column is scaled separately; contrast with Figure 2). The key above the heatmap shows the values indicated by different colours. The column-normalised heatmap allows us to see which categories of annotation are over-represented (relative to the total number of variants in the column/category) in the REFSEQ annotations for each category (i.e. column) of ENSEMBL annotation. Ideally, all of the dark red squares would lie on the diagonal, with white squares on the off-diagonals, indicating complete agreement in the annotations when using the two transcript sets. Compare with Additional file 1: Table S1, which provides the numbers used for this heatmap. Categories are ordered as per Table 1.

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