Table 2.

Numer of called variants and after sequential variant filtering process for each sample.

Filtering	S1a	S1b	S2	S3a	S3b	S4	S5a	S5b	S6	S7a	S7b	S8	S9	S10	S11
On target (VarDict − VarScan2)	298,250 173,072	363,209 101,637	239,526 266,542	286,381 200,507	241,135 453,494	382,519 119,025	231,469 263,604	312,808 245,467	276,040 273,296	293,494 176,720	315,825 171,718	274,664 317,568	191,603 720,791	223,731 261,383	302,540 172,629
Intersection	48,715	44,246	49,871	51,066	70,617	49,399	52,849	61,889	62,644	53,951	51,705	58,201	64,366	50,684	53,268
6pb indels	48,187	43,598	49,246	50,477	69,885	48,451	52,286	61,126	61,954	53,382	50,880	57,646	63,757	50,157	52,621
1000G mask	35,864	31,825	37,231	37,437	55,243	35,592	39,619	47,635	48,200	40,621	38,732	44,829	50,966	37,963	39,983
DP > 50	34,091	27,692	36,459	35,706	54,052	31,989	38,734	45,779	46,668	37,906	35,927	42,349	49,958	33,123	36,816
QUAL > 25	33,771	27,346	35,991	35,272	53,184	31,542	38,295	45,035	45,851	37,388	35,353	41,439	48,835	32,584	36,282
LoF & missense	18,476	15,154	19,998	18,929	31,534	18,100	21,148	26,962	27,596	22,103	20,585	24,283	28,888	18,518	21,472
gnomAD < 0.001	12,135	10,119	13,562	11,980	24,001	12,871	14,427	20,553	21,178	16,281	14,781	17,977	21,910	12,711	15,634
CADD > 15	9,035	7,904	10,085	8,864	19,044	9,994	10,828	16,271	16,808	12,662	11,077	13,887	17,086	9,547	12,155
GERP > 2	7,787	6,771	8,703	7,604	16,486	8,582	9,374	13,979	14,498	10,953	9,528	11,976	14,633	8,161	10,409
VD ≥ 3	6,977	6,086	7,446	6,528	14,473	7,720	8,560	12,509	13,231	9,764	8,181	9,719	11,024	5,162	8,991
Candidate genes	174	177	174	172	319	219	187	276	275	226	255	263	243	144	229

The last step where the causal somatic variant is retained is shown in bold.