Table 3.

Number of SNPs and Indels called by SAMtools and GATK

Number of variants	Unfiltered SNP		Filtered SNP		Unfiltered indel		Filtered indel
	SAMtools	GATK	SAMtools	GATK	SAMtools	GATK	SAMtools	GATK
100	1,020,180	492,537	183,178	103,790	91,216	53,722	22,058	11,750
101	1,073,008	518,360	181,294	102,548	93,768	56,052	21,935	11,474
102	930,610	456,647	179,665	100,100	82,297	48,705	21,764	11,242
103	1,066,604	458,137	177,006	95,249	86,249	46,024	20,276	9,479
Multiple samples of pedigree I	2,557,705	2,396,362	169,315	260,117	210,415	153,486	37,415	32,228
200	1,290,000	870,536	140,444	82,796	85,664	76,129	17,204	9,612
201	1,624,699	190,435	141,757	79,148	110,845	84,310	17,363	8,887
202	1,631,100	723,156	149,358	104,198	111,435	65,608	18,524	12,024
Multiple samples of pedigree II	4,013,542	2,265,075	190,882	137,137	245,998	194,616	22,765	24,739
SNP: Single nucleotide polymorphism, Indel: Insertion and deletion