Identification of genomic indels and structural variations using split reads

BMC Genomics

Table 3 Trio-array CGH validation of result. ^{1, 2}

t _n ³	2	3	4	5	6	7
True positive	48	23	17	12	9	7
Positive	76	27	20	15	11	9
Positive predictive value ⁴	0.63	0.85	0.85	0.80	0.82	0.78

Notes:
1. Only deletions longer than 50 bp called for an YRI individual (NA19240) from the 1000 Genomes Project are selected (randomly) for the trio-array CGH validation. Due to the data usage restriction, only validation results for deletions in chromosome 1 are used.
2. Not every validation test yields definite result. Inconclusive results are excluded from this table.
3. t_n, threshold on the number of supportive reads.
4. Positive predictive value = True positive/Positive.

ISSN: 1471-2164