Table 1.

Illustration of the Data Reduction at Each Step from Raw Reads to a Final Set of Mutated Loci

	Data remaining at the end of step
Filtering step	Disease/normal pair	Family trio BH1019	Family trio BH2041	Family trio BH2688
Number of reads from proband/diseased tissue	118,414,556	84,201,820	75,877,750	103,527,644
Number of 27-mers in proband/diseased tissue	911,738,627	795,477,167	517,272,851	1,088,610,020
Number of k-mers with count >10	77,903,885	61,805,320	64,719,150	113,066,951
Remove vector sequence	77,898,848	61,800,798	64,713,995	113,062,417
Eliminate k-mers found in reference GRC37 exome	17,821,359	9,385,347	10,730,208	50,535,681
Eliminate k-mers found in parent exomes/normal tissue	10,568	65,352	20,130	2,006
Identify reads containing k-mers	32,829 reads	148,496	46,454	4,404
Remove reads containing vector	15,260	125,648	38,799	2,760
Number of contigs after assembly	2,147	13,189	3,755	359
Number of contigs with >3 reads after merging contigs	279 contigs	1,437	701	71
Identify variants covered by reads from normal tissue	55 contigs	5	6	2
Keep variants with >5% coverage	42 variants	5	6	2
Find variants in coding regions	14 variants	3	3	1
Remove synonymous SNPs	10 variants	2	3	1