Table 2.

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

Pipeline	F1_Score	Recall	Precision	TOTAL	TP	FN	FP	FP.gt	FP.al
bwa-none-freebayes	0.991090	0.986208	0.996020	22,332	22,024	308	88	68	0
bwa-abra-freebayes	0.990910	0.986117	0.995749	22,330	22,020	310	94	75	0
bwa-gatk-freebayes	0.991157	0.986208	0.996155	22,332	22,024	308	85	67	0
bwa-none-gatk	0.988222	0.981314	0.995228	22,316	21,899	417	105	71	0
bwa-abra-gatk	0.988245	0.981447	0.995138	22,315	21,901	414	107	72	0
bwa-gatk-gatk	0.988063	0.981397	0.994820	22,308	21,893	415	114	72	0
bowtie-none-freebayes	0.943192	0.898413	0.992669	22,306	20,040	2266	148	105	0
bowtie-abra-freebayes	0.989173	0.985115	0.993265	22,305	21,973	332	149	106	0
bowtie-gatk-freebayes	0.942454	0.897206	0.992508	22,297	20,005	2292	151	101	0
bowtie-none-gatk	0.974657	0.956364	0.993663	22,298	21,325	973	136	88	0
bowtie-abra-gatk	0.974633	0.956319	0.993663	22,298	21,324	974	136	88	0
bowtie-gatk-gatk	0.974679	0.956407	0.993663	22,297	21,325	972	136	87	0