Fig. 1

Workflow of the nanotatoR pipeline: The nanotatoR pipeline is divided into 3 layers. Input Layer: Takes as input the OGM text or Smap file. Annotation Layer: The annotation layer comprises of five methods. The method that extracts the overlapping genes and the genes near (downstream and upstream) takes as input a BED file, and calculates the overlap percentage and the distance between nearest genes and SV using chromosomal locations. Next, the frequency calculation function calculates external and internal frequency taking DGV, DECIPHER and BNDB database as input for external frequency calculation, while input solo files, merged to form the internal frequency database, are taken as input to calculate the internal frequency. If RNA-Seq data is available, the expression count matrix is taken as input. Finally, output from all these methods as well as a primary gene list created from terms, is integrated, filtered based on quality criteria and written into an Excel file. Output Layer: The output is an Excel workbook, with each tab representing different SV types. The output files and number of tabs depend on the sample type and enzyme type: Singleton samples have 5 tabs for DLE and 6 tabs for SVmerge; 6 tabs for DLE and 7 tabs for SVmerge are created for dyad analyses; Trio analyses have 9 tabs for DLE and 10 tabs for SVmerge