Table 3.

Concordance between SNP chip and NGS data across all three duplicate removal methods are nearly identical

		Chip data
		homref	het	homalt
	homref	99.97	0.18	0.16
No dup	het	0.01	99.81	0.13
	homalt	0.02	0.01	99.71
	homref	99.97	0.19	0.14
Picard	het	0.01	99.80	0.14
	homalt	0.02	0.01	99.71
	homref	99.97	0.19	0.16
SAMTools	het	0.01	99.80	0.13
	homalt	0.02	0.01	99.71
	homref	99.91	0.06	0.18
No dup ACMG	het	0.02	99.94	0.07
	homalt	0.08	0.00	99.76
	homref	99.91	0.06	0.18
Picard ACMG	het	0.02	99.94	0.08
	homalt	0.08	0.00	99.75
	homref	99.91	0.06	0.18
SAMTools ACMG	het	0.02	99.94	0.07
	homalt	0.08	0.00	99.76

We compared the genotypes from NGS and matched SNP chip data to see if concordance varied by duplicate removal approaches. We performed this comparison for all variants and for ACMG variants only. Reported values are the percentage of total SNP chip genotypes called for a particular group (e.g., homozygous reference) that were correctly called by NGS for a given group. Exactly 99.97 % of genotypes called homozygous reference by SNP chip were also called homozygous reference by NGS across no dup, picard, and SAMTools. Similarly, 99.91 % of ACMG genotypes called homozygous reference by SNP chip were called identically by NGS. In the Table, homref: homozygous for the reference allele, het: heterozygous, and homalt: homozygous for an alternate allele