Table 3.

Comparison of noninvasive fetal variant calling pipelines in family G1 – Indels.

Pipeline	F1_Score	Recall	Precision	TOTAL	TP	FN	FP	FP.gt	FP.al
bwa-none-freebayes	0.722148	0.656098	0.802985	410	269	141	66	62	0
bwa-abra-freebayes	0.843710	0.805825	0.885333	412	332	80	43	41	0
bwa-gatk-freebayes	0.749669	0.695332	0.813218	407	283	124	65	58	0
bwa-none-gatk	0.961586	0.934940	0.989796	415	388	27	4	4	0
bwa-abra-gatk	0.964064	0.937349	0.992347	415	389	26	3	3	0
bwa-gatk-gatk	0.962779	0.934940	0.992327	415	388	27	3	3	0
bowtie-none-freebayes	0.736698	0.658537	0.835913	410	270	140	53	49	0
bowtie-abra-freebayes	0.864385	0.827670	0.904509	412	341	71	36	34	0
bowtie-gatk-freebayes	0.805851	0.737226	0.888563	411	303	108	38	35	0
bowtie-none-gatk	0.940881	0.901205	0.984211	415	374	41	6	6	0
bowtie-abra-gatk	0.940881	0.901205	0.984211	415	374	41	6	6	0
bowtie-gatk-gatk	0.944862	0.908434	0.984334	415	377	38	6	6	0