Challenges in exome analysis by LifeScope and its alternative computational pipelines

BMC Research Notes

Table 3 Counts of SNPs identified in the family exomes present in the datasets of known variants

	LifeScope	LifeScope-GATK	MAQ-GATK	SHRiMP-GATK	BFAST-GATK
Proband
Total	38,626	60,313	49,483	67,669	43,536
dbsnp138	37,312	58,342	48,538	65,185	42,909
1000G	35,511	54,745	46,706	62,778	42,030
esp6500	31,319	29,745	26,041	27,386	25,169
In target regions	21,837	19,530	16,958	17,082	15,856
dbsnp138	20,892	18,869	16,707	16,768	15,688
1000G	19,504	17,954	16,260	16,304	15,321
esp6500	17,894	16,469	14,912	14,891	14,138
Mother
Total	35,267	43,831	28,032	38,711	26,898
dbsnp138	34,075	42,778	27,641	38,337	26,626
1000G	32,455	40,316	26,472	36,856	26,170
esp6500	29,095	26,101	17,909	23,348	19,139
In target regions	20,995	17,697	12,566	15,477	12,722
dbsnp138	20,099	17,296	12,470	15,359	12,623
1000G	18,806	16,459	12,143	14,939	12,384
esp6500	17,281	15,099	11,163	13,658	11,469
Father
Total	36,350	46,822	36,798	42,486	27,949
dbsnp138	35,106	45,723	36,209	42,193	27,669
1000G	33,381	42,939	34,777	40,782	27,204
esp6500	29,765	26,728	22,177	24,458	19,715
In target regions	21,254	17,936	14,972	15,760	13,033
dbsnp138	20,348	17,531	14,827	15,661	12,931
1000G	19,015	16,668	14,447	15,296	12,692
esp6500	17,457	15,323	13,326	14,042	11,756

For each exome and the approach a total number of all identified SNPs and the SNPs that are only in the targeted regions are shown in italic

ISSN: 1756-0500