A study on fast calling variants from next-generation sequencing data using decision tree

BMC Bioinformatics

Table 7 Comparison of SNP and indel calls on the WGS data of the Ashkenazim Trio and the Chinese sample for the four callers

	benchmark	Fuwa	Platypus	GATK-UG	GATK-HC	SAMtools
a. NA24149
Total	3,600,577	4,596,629	4,936,516	5,078,361	4,962,252	5,121,162
SNP	3,062,103	3,773,197	3,741,864	4,222,373	4,073,476	4,052,727
Indel	538,474	823,432	1,194,652	855,988	888,776	1,068,435
SNP Recall(%)	–	99.64	94.10	99.88	99.88	99.55
SNP Precision(%)	–	80.86	77.00	72.44	75.08	75.22
Indel Recall(%)	–	91.99	97.26	95.51	96.66	80.30
Indel Precision(%)	–	60.16	43.84	60.08	58.57	40.47
b. NA24143
Total	3,638,487	4,683,584	5,047,869	5,185,325	5,069,960	5,231,986
SNP	3,089,689	3,848,083	3,818,763	4,304,521	4,153,126	4,127,152
Indel	548,798	835,501	1,229,106	880,804	916,834	1,104,834
SNP Recall(%)	–	99.65	94.12	99.89	99.90	99.55
SNP Precision(%)		80.01	76.15	71.70	74.32	74.53
Indel Recall(%)	–	91.86	97.29	95.73	96.92	80.38
Indel Precision(%)		60.34	43.44	59.64	58.01	39.92
c. NA24385
Total	3,650,031	4,765,697	4,425,266	4,839,691	4,685,838	5,191,731
SNP	3,101,709	3,942,411	3,452,047	3,987,637	3,803,199	4,123,595
Indel	548,322	823,286	973,219	852,054	882,639	1,068,136
SNP Recall(%)	–	99.91	88.60	99.88	99.92	99.67
SNP Precision(%)		78.60	79.60	77.69	81.49	74.97
Indel Recall(%)	–	91.39	90.14	95.98	98.21	81.96
Indel Precision(%)		60.87	50.79	61.77	61.01	42.07
d. NA24631
Total	3,655,030	4,599,648	4,935,176	4,987,136	4,871,278	4,667,766
SNP	3,195,050	3,743,038	3,647,691	4,079,102	3,901,018	3,900,109
Indel	459,980	856,610	1,287,485	908,034	970,260	767,657
SNP Recall(%)	–	99.48	93.98	99.93	99.92	99.67
SNP Precision(%)		84.92	82.32	78.27	81.84	81.65
Indel Recall(%)	–	93.52	97.53	97.53	99.54	12.48
Indel Precision(%)		50.22	34.84	49.41	47.19	7.48

ISSN: 1471-2105