Fig. 4

Variant distribution for the singleton NA12878 sample. a Unfiltered and filtered variants distribution in DLE and SVmerge datasets: The total number of unfiltered variants for NA12878 DLE are 10,087, out of which 9584 variants are filtered using nanotatoR criteria (found in self molecules, passed chimeric score threshold). For NA12878 SVmerge, out of 6814 variants, 6201 pass the filtration. Mismatches were not considered in this analysis but are shown in Table S7. b SV distribution in the NA12878 DLE and SVmerge filtered datasets: Deletions (dark blue), insertions (light blue), duplications (grey) and inversions (orange) numbers are as shown in the pie charts. Bottom table shows distribution of SVs by type in percentages. For DLE, the majority of the identified SVs were insertions (64.9%), followed by deletions (33.5%), inversions (1.1%) and finally duplications (0.5%). While the total number of variants called is different between DLE and SVmerge, a similar pattern is seen in the SVmerge dataset. Many more duplications and inversions were called in the dual labeling than single DLE labeling method