Table 2.

Concordance of Astrolabe, Aldy, and Stargazer on test cases (N = 154) homozygous for SNV-defined star alleles at 30×.

	Astrolabe		Aldy		Stargazer
	Run 1	Run 2	Run 1	Run 2
Match	142 (92%)	152 (99%)	148 (96%)	149 (97%)	135 (88%)
Mismatch	9 (6%)	1 (1%)	4 (3%)	3 (2%)	19 (12%)
Ungenotyped	3 (2%)	1 (1%)	2 (1%)	1 (1%)	0

Inconsistencies
Algorithm	Challenges	Discordant cases	Notes
Astrolabe	Undefined suballeles	*2.014, *4.002, *4.003, *4.007, *4.009, *52.002, *56.003	Ambiguous calls or miscalls
	Indel-defined alleles	*18.001	Position discordance with database
Aldy	Undefined suballeles	*12.002, *71.003	Ambiguous calls or miscalls
	Indel-defined alleles	*18.001, *20.001, *38.001	Position discordance with database
Stargazer	Indel-defined alleles	*20.001	Position discordance with database
	Alleles with unknown or uncertain function and/or rare alleles	18 alleles including *30.001, *37.001, *58.001, *52.001, *64.001, *65.001, and *73.001 (Supplementary Data Set 2)	Stargazer reports background alleles as the main haplotypes in these cases. Exact haplotypes (matching truthset) in the sample(s) are reported among other candidate haplotypes. (See discussion for details)

The complete list of genotypes called per sample is provided in Supplementary Data Set 2.

Run 1 and Run 2 indicate results before and after defining missing suballeles in the allele tables, respectively. There was only one run for Stargazer as it does not typically call suballeles.