Table 2. Cumulative application of filters.

		1a: Ins/del BRCA HP		1→2b: Cov<38		(1+2)→3c: VAF<0.25		(1+2+3)→4d: Fcov=0 or Rcov=0		(1+2+3)→5 e: FQ<30 & RQ<30		(1+2+3)→6f: Total Q <30
	Before filters	In	Out	In	Out	In	Out	In	Out	In	Out	In	Out
Training Set
FP	4037	2307	1730	2210	97	512	1698	9	503	228	284	227	285
TP	223	212	11	202	10	202	0	200	2	201	1	200	2
Sensitivity		0.951		0.953		1.000		0.990		0.995		0.990
Specificity		0.429		0.042		0.769		0.982		0.555		0.557
Validation Set
FP	1471	872	599	872	0	168	704	3	165	59	109	59	109
TP	123	122	1	122	0	122	0	121	1	122	0	122	0
Sensitivity		0.992		1.000		1.000		0.992		1.000		1.000
Specificity		0.407		0.000		0.807		0.982		0.649		0.649

Variants retained (In) and discarded (Out) by the application of:

^afilter 1: insertion or deletion covered by the BRCA HP assay.

^bfilter 2: coverage below 38, to variants retained by filter 1.

^cfilter 3: variant allele frequency below 0.25, to variants retained by filters 1 and 2.

^dfilter 4: variant forward coverage or variant reverse coverage equal to 0, to variants retained by filters 1, 2, and 3.

^efilter 5: variant forward quality and variant reverse quality below 30, to variants retained by filters 1, 2, and 3.

^ffilter 6: total variant quality below 30, to variants retained by filters 1, 2, and 3.