KAGE: fast alignment-free graph-based genotyping of SNPs and short indels

Table 3 Results from genotyping HG002

	Indels recall	Indels precision	Indels F1	SNPs recall	SNPs precision	SNPs F1	Runtime	Memory usage
KAGE	0.582	0.908	0.709	0.929	0.981	0.955	12 min	18 GB
KAGE + GLIMPSE	0.594	0.894	0.713	0.948	0.99	0.968	1.4 hours	18 GB
PanGenie	0.561	0.926	0.699	0.905	0.979	0.941	3.9 hours	111 GB
Bayestyper	0.485	0.993	0.652	0.834	0.997	0.908	7.9 hours	30 GB
Malva	0.537	0.856	0.659	0.849	0.921	0.883	14.9 hours	50 GB
Graphtyper	0.568	0.941	0.708	0.909	0.993	0.949	5.1 hours	23 GB
GATK	0.898	0.96	0.928	0.966	0.981	0.973	9.0 hours	64 GB

ISSN: 1474-760X