Table 1.

Summary of Variant Calling for Eight Pipelines for the WGS Sample

Dataset	Total calls	TP	FP	FN	Specificity	Sensitivity	F1 score
Whole genome SNVs
NIST v2.18 Gold Standard	2,740,732
BWA‐MEM‐MEM + FreeBayes	2,744,545	2,738,200	6,345	2,532	0.99769	0.99908	0.99838
BWA‐MEM + HaplotypeCaller	2,748,582	2,738,426	10,156	2,306	0.99631	0.99916	0.99773
BWA‐MEM + SAMtools fast	2,748,866	2,738,489	10,377	2,243	0.99622	0.99918	0.99770
BWA‐MEM + SAMtools normal	2,736,410	2,732,882	3,528	7,850	0.99871	0.99714	0.99792
GEM3 + FreeBayes	2,742,937	2,735,581	7,356	5,151	0.99732	0.99812	0.99772
GEM3 + HaplotypeCaller	2,745,423	2,738,414	7,009	2,318	0.99745	0.99915	0.99830
GEM3 + SAMtools fast	2,749,554	2,736,718	12,836	4,014	0.99533	0.99854	0.99693
GEM3 + SAMtools normal	2,736,871	2,732,313	4,558	8,419	0.99833	0.99693	0.99763
Whole genome deletions
NIST v2.18 Gold Standard	85,958
BWA‐MEM + FreeBayes	82,263	75,674	6,589	10,284	0.91990	0.88036	0.89970
BWA‐MEM + HaplotypeCaller	86,323	84,789	1,534	1,169	0.98223	0.98640	0.98431
BWA‐MEM + SAMtools fast	77,671	68,591	9,080	17,367	0.88310	0.79796	0.83837
BWA‐MEM + SAMtools normal	77,712	68,615	9,097	17,343	0.88294	0.79824	0.83846
GEM3 + FreeBayes	81,602	76,002	5,600	9,956	0.93137	0.88418	0.90716
GEM3 + HaplotypeCaller	86,132	84,783	1,349	1,175	0.98434	0.98633	0.98533
GEM3 + SAMtools fast	80,905	69,096	11,809	16,862	0.85404	0.80383	0.82818
GEM3 + SAMtools normal	80,955	69,124	11,831	16,834	0.85386	0.80416	0.82826
Whole genome insertions
NIST v2.18 Gold Standard	84,583
BWA‐MEM + FreeBayes	78,592	73,890	4,702	10,693	0.94017	0.87358	0.90565
BWA‐MEM + HaplotypeCaller	84,521	83,473	1,048	1,110	0.98760	0.98688	0.98724
BWA‐MEM + SAMtools fast	79,762	69,389	10,373	15,194	0.86995	0.82037	0.84443
BWA‐MEM + SAMtools normal	79,762	69,396	10,366	15,187	0.87004	0.82045	0.84452
GEM3 + FreeBayes	78,417	73,154	5,263	11,429	0.93288	0.86488	0.89760
GEM3 + HaplotypeCaller	83,973	83,189	784	1,394	0.99066	0.98352	0.98708
GEM3 + SAMtools fast	92,775	71,928	20,847	12,655	0.77530	0.85038	0.81111
GEM3 + SAMtools normal	92,795	71,938	20,857	12,645	0.77524	0.85050	0.81113

TP, true positives; FP, false positives; FN, false negatives; specificity, number of TP calls as a proportion of total calls; sensitivity, number of TP calls as a proportion of the number of NIST reference set calls; F1‐score, measure of overall accuracy calculated as (2 × TP)/((2 × TP) + FP + FN).