Extract Segments Tool (Borland Genetics)

The Extract Segments tool is an advanced reconstruction tool packaged in the Borland Genetics DNA toolkit.

This tool is one of two tools that requires as input a .csv export from DNA Painter. Note that the export is accomplished from the Settings wheel of a DNA Painter profile, by selecting “All Segment Data” and then clicking on “CSV file” on the top left. DNA Painter Data Backup files are not currently compatible with Borland Genetics.

Extract Segments effectively creates a filter to be applied to a Mono kit to extract segments that are inherited from a selected source (as identified in the legend of a DNA Painter profile). The boundaries of the segments in the DNA Painter file can be either indicated using Build 36 (GEDmatch) or Build 37 (GEDmatch Genesis and others) coordinates, but should be consistent throughout the profile. The Extract Segments tool automatically converts the coordinates to Build 37 if necessary.

Generally the boundaries of segments are determined using a process called Visual Phasing, which can be accomplished via a number of different tools including the popular Fox spreadsheet and the GedMatch Matching Segments and/or 1:1 Compare tools. The output from the Extract Segments tool is a Mono kit data containing genetic data only in regions as prescribed by the DNA Painter filter selected. This output is said to be “bound” because all other data in the kit is replaced by white noise filler data designed so that these regions cannot possibly trigger cousin matches with other kits. An accompanying Reconstructed Segments file is created memorializing the selected segment boundaries (converted to Build 37 coordinates as applicable).

Note that since output of this tool contains white noise, the output Mono kit is not appropriate for use with ethnicity tools on GedMatch (or elsewhere), without applying a further transformation/selection process using GedMatch’s Lazarus tool.

As this tool is among the most versatile tools included in Borland Genetics, video tutorials have been created illustrating a wide variety of uses and featured on the Borland Genetics YouTube channel and in the Borland Genetics Users Facebook Group. The Extract Segments tool is also a key tool used to execute the Phased Pseudo-Sibling Method.