Fig. 5

Calling medium sized indels with Pindel. Pindel [29] was used to detect structural variants in exome sequencing data of n = 54 probands. a Average number of variants by size detected by Pindel within the target region +/- 50 bases or in all regions. b Percentage of variants within or outside the target region. c Comparison of Pindel variants to the number of indels called by the variant caller broken down by variant size. d Percentage of Pindel variants within or outside the target regions +/- 50 bases that were also called by the variant caller. e Estimated allele frequencies based on a founder population of 106 parents. f Phasing of variants detected in the probands considering all variants or only variants that were unique to Pindel and that were rare. g Average number of Pindel variants after each step of filtration left for continued evaluation