Improving somatic exome sequencing performance by biological replicates

BMC Bioinformatics

Table 1 Performance scores of the within-center approach for center replicates of FD

	TP	FP	FN	Precision	Recall	F1
FD_bwa_mutect_m ≥ 1	1003	525	156	0.656	0.865	0.747
FD_bwa_mutect_m ≥ 2	900	2	259	0.998	0.777	0.873
FD_bwa_mutect_m ≥ 3	749	0	410	1.000	0.646	0.785
FD_bowtie_mutect_m ≥ 1	988	565	171	0.636	0.852	0.729
FD_bowtie_mutect_m ≥ 2	875	2	284	0.998	0.755	0.860
FD_bowtie_mutect_m ≥ 3	727	0	432	1.000	0.627	0.771
FD_bwa_strelka_m ≥ 1	1037	2808	122	0.270	0.895	0.414
FD_bwa_strelka_m ≥ 2	927	20	232	0.979	0.800	0.880
FD_bwa_strelka_m ≥ 3	785	3	374	0.996	0.677	0.806
FD_bowtie_strelka_m ≥ 1	937	539	222	0.635	0.808	0.711
FD_bowtie_strelka_m ≥ 2	792	5	367	0.994	0.683	0.810
FD_bowtie_strelka_m ≥ 3	643	3	516	0.995	0.555	0.712
FD_bwa_ss_m ≥ 1	948	1013	211	0.483	0.818	0.608
FD_bwa_ss_m ≥ 2	816	96	343	0.895	0.704	0.788
FD_bwa_ss_m ≥ 3	677	9	482	0.987	0.584	0.734
FD_bowtie_ss_m ≥ 1	918	1009	241	0.476	0.792	0.595
FD_bowtie_ss_m ≥ 2	793	97	366	0.891	0.684	0.774
FD_bowtie_ss_m ≥ 3	661	15	498	0.978	0.570	0.720

The notation "m" is used for multiple detection results. It indicates how many times a variant has been captured in pipelines generated using data from FD replicates. For example, "FD_bwa_mutect_m ≥ 2" indicates the scores of the variants detected in two or more bwa_mutect pipelines in FD replicates

ISSN: 1471-2105