| Â | ANV + VEP | ANV | VEP | Exact | Category | ANV match | VEP match | Overall | Overall |
|---|
| Â | Â | Â | Â | match | match | rate (%) | rate (%) | category match | exact match |
|---|
| Â | Â | Â | Â | Â | Â | Â | Â | rate (%) | rate (%) |
|---|
LOF total | 104,915 | 77,527 | 96,761 | 68,284 | 69,373 | 88.08 | 70.57 | 66.12 | 65.09 |
Frameshift | 19,021 | 15,822 | 16,685 | 13,486 | - | 85.24 | 80.83 | - | 70.90 |
Stop gained | 16,758 | 14,960 | 16,146 | 14,348 | - | 95.91 | 88.86 | - | 85.62 |
Stop lost | 1,113 | 906 | 1,077 | 870 | - | 96.03 | 80.78 | - | 78.17 |
All splicing | 69,112 | 45,839 | 62,853 | 39,580 | - | 86.35 | 62.97 | - | 57.27 |
MISSENSE total | 350,806 | 324,242 | 347,752 | 318,056 | 321,188 | 98.09 | 91.46 | 91.56 | 90.66 |
Inframe indel | 9,455 | 8,650 | 6,600 | 5,795 | - | 66.99 | 87.80 | - | 61.29 |
Missense | 343,284 | 315,592 | 339,953 | 312,261 | - | 98.94 | 91.85 | - | 90.96 |
Initiator codon | 1,199 | 0 | 1,199 | 0 | - | - | 0.00 | - | 0.00 |
SYNONYMOUS and | Â | Â | Â | Â | Â | Â | Â | Â | Â |
OTHER CODING total | 182,120 | 172,463 | 175,483 | 165,643 | 165,826 | 96.05 | 94.39 | 91.05 | 90.95 |
Synonymous | 181,873 | 172,463 | 175,053 | 165,643 | - | 96.05 | 94.62 | - | 91.08 |
Stop retained | 203 | 0 | 203 | 0 | - | - | 0.00 | - | 0.00 |
Other coding | 227 | 0 | 227 | 0 | - | - | 0.00 | - | 0.00 |
ALL LOF | 104,915 | 77,527 | 96,761 | 68,284 | 69,373 | 88.08 | 70.57 | 66.12 | 65.09 |
ALL LOF and MISSENSE | 455,721 | 401,769 | 444,513 | 386,340 | 390,561 | 96.16 | 86.91 | 85.70 | 84.78 |
ALL EXONIC | 637,841 | 574,232 | 619,996 | 551,983 | 556,387 | 96.13 | 89.03 | 87.23 | 86.54 |
- This table summarises the number of annotations that match between the ANNOVAR and VEP results (when using ENSEMBL transcripts) for each exonic category of annotation. It shows the number of variants given each type of annotation by when using (i) either ANNOVAR or VEP (‘ANV+VEP’; union), (ii) ANNOVAR (‘ANV’) and (iii) VEP (‘VEP’). It also shows the number of variants that have exact matching annotations (i.e. exactly the same annotation from both tools; intersection), and category-matching annotations (i.e. annotations from the two tools in the same high-level category – LoF, missense, synonymous and other coding – even if not an exact match). Columns six and seven show the match rate for each tool, which gives the percentage of matching annotations for an annotation term from ANNOVAR and VEP, respectively, relative to the total number of annotations in the category from the particular software tool. Column eight gives the percentage of variants with annotations from ANNOVAR and VEP in the same high-level category (overall category match rate). Column nine shows the overall exact match rate, which is the percentage of variants with an annotation from either ANNOVAR or VEP (‘ANV+VEP’) that have an exactly matching annotation from the two tools. Here, the specific annotations from equivalent terms for ANNOVAR and VEP have been aggregated to enable the comparison (see Additional file 1: Table S4). The final three rows of the table show aggregate counts and match rates for all loss-of-function categories, all LoF and missense categories and all exonic categories, respectively. Note that the all splicing category for VEP comprises 5,011 splice acceptor variants, 8,544 splice donor variants and 49,298 more general splice region variants. ANNOVAR, in contrast, only has one general splicing category, and does not distinguish between acceptor, donor and other splicing variants.
