Skip to main content

Table 1 aVariant calling results: before filtering

From: A clinically validated whole genome pipeline for structural variant detection and analysis

bucket TP FP FN sensitivity
100–1000 2233 202 965 0.69825
1000-10,000 613 139 61 0.90950
10,000–100,000 48 97 3 0.94118
100,000+ 5 84 0 1
  1. a The analysis has been performed using Genome in a Bottle truth dataset NA24385 (http://tinyurl.com/GIABSV06). Since the truth set was built on top of hg19, we had to lift over results from hg19 to hg38 which dropped some variants. In addition, in order to not be biased we have only compared SVs that were liftable from hg38 to hg19 (to make sure we don’t have any false, false positives). We also removed calls made in non-unique areas and calls < 100 bp