Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

Table 3 De novo single-nucleotide variants (SNVs) were detected in two families contained within the 15 study exomes.

	Number of putative de novo coding non-synonymous or nonsense SNVs detected
Family 1	Without using the grandparents as a filter	Using the grandparents as a filter
Child A	241	1
Child B	211	0
Child C	102	6
Child D	242	3
Family 2
Child A	49	NA^a
Child B	41	NA^a

^aN/A, no grandparent available.
Family 1 had a grandparent available for filtering purposes, whereas family 2 did not. To minimize false positives in the pool of SNVs associated with each child, only highly concordant SNVs were used (SNVs detected by all five pipelines). To construct a comprehensive set of SNVs for each parent, and hence increase filtering accuracy, false negatives for parent SNVs were reduced by taking the union of all SNV calls from all five pipelines.

ISSN: 1756-994X