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Fig. 3 | BMC Bioinformatics

Fig. 3

From: SVAT: Secure outsourcing of variant annotation and genotype aggregation

Fig. 3

Examples of mismatches between SVAT and VEP while annotating deletions. a Two examples of deletions that impact CAP1 gene as they are annotated by VEP. 9-bp deletion that engulfs the stop-codon (shown in red) are annotated by VEP. This variant is annotated by VEP only as “stop_lost”. On the other hand, the 4-bp deletion that deletes only 1 base pair from the stop-codon is annotated as “frame_shift, stop_lost”. b Similar to (a), the start-codon impacting variants are annotated by VEP as “start_lost” for an 8-bp deletion (top) and as “start_lost, frameshift” for a 9-bp deletion (bottom). VEP does not assign “frame_shift” term when the start-codon is engulfed in the variant. In both of these cases, SVAT assigns both frame_shift and start_lost terms. c Examples of two deletions that are discordantly annotated by SVAT and VEP. For both deletions, SVAT annotates by “frameshift_variant, stop_gain” whereas VEP annotates the 2-bp deletion (left) as frameshift and the 5-bp deletion (right) as “frameshift_variant, stop_gain”. 2-bp deletion (left) also causes a stop-gain at the junction where frame contains a “TGA” stop-codon. This is detected by SVAT while VEP does not report the stop-gain. It should, however, be noted that these deletions are both in HIGH impact class and would be picked up as candidates in downstream analyses. d An example of a stop_gain that is detected by VEP and missed by SVAT. The deletion that ends right at the splice junction site creates a junction with a stop codon. Both mutations are in HIGH impact class as this is also a frameshift mutation. e Another example of a downstream stop-codon that is missed by SVAT and picked up by VEP. The 8-bp deletion engulfs stop-codon and creates a new frame such that a downstream stop-codon (“TGA” stop codons as shown in figure) is created within the new coding frame. This mutation is marked as HIGH-impact by VEP and by SVAT

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