Challenges in exome analysis by LifeScope and its alternative computational pipelines

BMC Research Notes

Table 6 SNPs annotated in ClinVar and COSMIC databases per method and per person

	LifeScope	LifeScope-GATK	MAQ-GATK	BFAST-GATK
Proband
ClinVar total	1328	1261	1116	1150
Deleterious variants	44;34pat + 10drug	42;33pat + 9drug	38;29pat + 9drug	34;27pat + 7drug
Deleterious at 15×	32;23pat + 9drug	38;28pat + 10drug	24;19pat + 5drug	21;15pat + 6drug
Loss going to 15×	27 %	9.5 %	37 %	38 %
COSMIC total	468	366	310	299
COSMIC variants at 15×	349	238	195	168
Loss going to 15×	25 %	35 %	37 %	44 %
Mother
ClinVar total	1288	1170	841	947
Deleterious variants	47;38pat + 9drug	41;33pat + 8drug	38;30pat + 8drug	36;30pat + 6drug
Deleterious at 15×	20;15pat + 5drug	30;24pat + 6drug	11;10pat + 1drug	11; 8pat + 3drug
Loss going to 15×	57 %	27 %	71 %	69 %
COSMIC total	395	292	197	194
COSMIC at 15×	231	124	73	63
Loss going to 15×	42 %	52 %	63 %	68 %
Father
ClinVar total	1248	1126	950	959
Deleterious variants	43;36pat + 7drug	37;31pat + 6drug	31;26pat + 5drug	36;30pat + 6drug
Deleterious at 15×	19;16pat + 3drug	26;22pat + 4drug	12;11pat + 1drug	11;9pat + 2drug
Loss going to 15×	56 %	30 %	61 %	69 %
COSMIC total	444	340	270	197
COSMIC at 15×	288	176	122	74
Loss going to 15×	35 %	37 %	55 %	62 %

Total number of identified variants in ClinVar is shown together with the number of patogenic (pat) and drug response (drug) variants. Counts of high confidence variants covered at least by 15\(\times\) are presented for both: ClinVar and COSMIC. A fraction of total variants which would be lost by going to a higher coverage is presented by a percentage

ISSN: 1756-0500