CooVar: Co-occurring variant analyzer

BMC Research Notes

Table 1 Comparison of GVs annotated with CooVar and VEP for human individual HG00732-200-37-ASM

	CooVar	VEP
Runtime	36m	37h 24m
Total reported GVs	4,158,840	4,043,939
Intronic/intergenic/UTR	4,133,885	4,019,490
Impacting protein-coding exon	24,955	24,449
Synonymous/stop retained	11,585	11,434
Missense	12,011	11,576
Conservative (%)^$	9,526 (79.3)	7,447 (64.3)
Non-conservative (%)⁺	2,485 (20.7)	2,110 (18.3)
Unknown consequence (%)	0 (0)	2,019 (17.4)
Splice donor/acceptor	97	184
Stop lost	47	46
Stop gained	137	134
Frameshift	470	490
Inframe	199	165
Other	0	31
Multiple*	409	389
ORF disrupted	782^¥	871^§

Each GV reported by CooVar (v0.05) and VEP (v2.6) was assigned to one (and only one) of the above categories. $ CooVar: Grantham score conservative or moderately conservative; VEP: SIFT benign; + CooVar: Grantham score moderately radical or radical; VEP: SIFT deleterious. * GVs assigned to more than one category due to differential impact on different transcripts. ¥ Presence of internal stop codon within the first 70% of ORF length, after applying all variants. § Predicted frameshift or stop gain variant within the first 70% of ORF length. Abbreviations: GV … genomic variation; ORF … open reading frame; VEP… Variant Effect Predictor; UTR… untranslated region.

ISSN: 1756-0500