Skip to main content

Advertisement

Table 2 Same transcripts, different software: ANNOVAR and VEP annotations for exonic variants

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

  ANV + VEP ANV VEP Exact Category ANV match VEP match Overall Overall
     match match rate (%) rate (%) category match exact match
         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          
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
  1. 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.