Measuring, visualizing, and diagnosing reference bias with biastools

Table 1 Number of balanced sites and different categories of biased sites on chromosome 20. The simulated WGS reads of HG002 are aligned by 8 different tools. The best results of balanced and Bias “Loss” are marked in bold and italic. The second best results are marked in bold

		Bowtie 2	BWA-MEM	BWA-MEM (-L 30)	Minimap2	Giraffe-linear	Giraffe-major	Giraffe-pop5	Giraffe-1KGP
SNV	Balanced	52,173	52,133	52,336	52,148	52,267	52,267	52,353	*52,402*
	Bias (loss)	2108	2084	1881	2028	1924	1911	1812	*1752*
	Bias (flux)	*495*	569	594	581	566	561	548	573
	Bias (local)	169	177	*158*	186	183	210	228	211
	Outliers	78	60	54	80	83	74	82	85
Gap	Balanced	10,386	10,143	*10,519*	10,213	10,308	10,323	10,336	10,358
	Bias (loss)	628	799	*435*	726	659	630	600	571
	Bias (flux)	*112*	146	150	160	137	143	139	142
	Bias (local)	*122*	165	149	161	151	156	177	180
	Outliers	22	17	17	10	15	18	18	19

ISSN: 1474-760X