Table 5.

Summary of coverage [depth of coverage (DP) assigned to a variant by GATK] for variants called by the different approaches in family exomes

Proband variants	All variants per method			Common 21,687 variants		Variants in COSMIC
Identification method	Coverage quartiles Q25,Med,Q75	Total #	Sites % ≥ 8×	Coverage quartiles Q25,Med,Q75	Sites % ≥ 8×	Coverage quartiles Q25,Med,Q75	Total #
LifeScope	12,25,46	38,626	87	16,28,46	92	11,28,51	89
LifeScope-GATK	7,14,24	60,313	75	14,21,30	95	16,22,35	21
MAQ-GATK	7,13,23	49,483	74	10,17,25	86	25,33,64	15
SHRiMP-GATK	6,16,34	67,669	72	21,32,50	98	15,52,120	22
BFAST-GATK	7,13,22	43,536	73	11,18,27	89	7,8,10	10

Mother variants	All variants per method			Common 13,995 variants		Variants in COSMIC
Identification method	Coverage quartiles Q25,Med,Q75	Total #	Sites % ≥ 8×	Coverage quartiles Q25,Med,Q75	Sites % ≥ 8×	Coverage quartiles Q25,Med,Q75	Total #
LifeScope	8,15,26	35,267	76	12,20,30	89	7,16,28	101
LifeScope-GATK	6,10,16	43,831	65	10,15,21	90	10,23,27	13
MAQ-GATK	6,10,15	28,032	61	6,10,15	66	25,32,61	6
SHRiMP-GATK	6,11,17	38,711	68	10,14,20	88	17,20,34	13
BFAST-GATK	5,9,14	26,898	58	2,12,16	74	5,6,8.5	6

Father variants	All variants per method			Common 11,483 variants		Variants in COSMIC
Identification method	Coverage quartiles Q25,Med,Q75	Total #	Sites % ≥ 8×	Coverage quartiles Q25,Med,Q75	Sites % ≥ 8×	Coverage quartiles Q25,Med,Q75	Total #
LifeScope	8,16,29	36,350	78	12,21,31	89	8,15,31.5	99
LifeScope-GATK	6,11,18	46,822	68	11,16,22	90	14,23,30	12
MAQ-GATK	6,10,17	36,798	66	8,12,18	76	34,57,94	5
SHRiMP-GATK	7,12,20	42,486	74	12,18,25	94	17,21,21	4
BFAST-GATK	6,9,15	27,949	61	7,11,17	73	8,12,17	93

Coverage is summarized as median and 1st and 3rd quartile showing a central tendency. This coverage tendency is presented for: all called variants, common variants called by all methods and approach-specific variants in COSMIC. An additional quality measure—a fraction of variants—covered at least by 8 reads is shown for each method for all and common variants