Borland Genetics Desktop Toolkit
From ISOGG Wiki
The Borland Genetics Desktop Toolkit is a free DNA software toolkit designed by Borland Genetics to assist in reconstructing genomes of deceased ancestors and relatives whose DNA is unavailable for testing via traditional means. The software allows users to design and implement custom DNA reconstruction workflows using a series of simple tools that operate on raw DNA resources. The toolkit was publicly released on October 30, 2018.
Original Tools (v1.5)
The Chameleon tool allows users to convert DNA resource between factory templates or onto custom templates. It operates in three modes. In the first mode, users can convert a raw DNA file from its original template to that of another DNA resource. For example, if you provide the tool with an AncestryDNA v1 kit and a 23andMe v5 kit, you can map either kit onto the template of the other. The second mode allows users to map two kits on different templates to a combined template consisting of all of the tested SNPs reported in either template. The third mode allows mapping to a shared template consisting only of SNPs shared by the templates of the two input kits.
Some tools require users to convert all input resources to a common template prior to use.
Basic phasing tools
Among the stand-alone phasing tools packaged in Borland Genetics include the Phoenix tool and its counterpart the Darkside tool, which reconstruct a partial or full phased parent kit using either relatives all on the same side or opposite side of the family as the reconstruction target, respectively. Both tools result in mono output, as they reconstruct portions of a single copy of the child donor's DNA.
The Missing Parent tool serves as a workflow to reconstruct the DNA of an unavailable parent by phasing the DNA of an available parent with the DNA of as many children of the two-parent couple as resources permit. If more than one child's kit is used as input, the resulting output is stereo. Otherwise, use of this tool with a single child will result in mono output.
The Two Parent Phasing tool is a simple workflow that phases a donor’s genome using data from both parents to significantly increase resolution of traditional phased output kits.
Advanced phasing tools
Borland Genetics includes two advanced phasing workflows that interact with output from visual phasing projects stored in DNA Painter profiles. These are the Reverse Phase and Extract Segments tools, both of which are essential component workflows for any complex reconstruction projects to be executed via the toolkit. Additionally, the toolkit provides direct access to unbound data from the tool's phasing engine via the Ultimate Phaser tool.
The Extract Segments tool effectively uses a DNA Painter ancestor group as a filter to be applied to a mono kit to extract segments that are inherited from the corresponding ancestor. The boundaries of the segments can be input or imported into DNAPainter using either Build 36 or Build 37 coordinates, as segment data is automatically converted to Build 37 prior to extraction. Output is “bound” because all extraneous data in the input kit is replaced by “white noise” designed to prevent triggering false cousin matches upon upload to GEDmatch.
The Reverse Phase tool accomplishes full paternal vs. maternal phasing of a donor’s chromosomes using DNA from a child rather than a parent. Unlike traditional phasing, the process is not fully automatic, and requires the additional step of a simplified visual phasing process using DNA Painter and the GEDmatch Matching Segments tool. Output may or may not include white noise depending on whether there were gaps between segments as painted (the distinction dictates whether or not the output is compatible with GEDmatch admixture tools).
The most frequent application of the Ultimate Phaser tool is to create full mono kits for use in visual phasing projects. These visual phasing seed kits should always be marked as research kits when uploaded to GEDmatch, as they do not represent the reconstruction of a single real person.
Output from the Ultimate Phaser (when applied to a parent and child) can be channeled to one the following three categories of phased data:
- Parent ∩ Child (all DNA shared between a parent and child, which will alternate between grandparent streams at recombination points determined via visual phasing)
- Parent x Child (sometimes referred to as the evil twin, all DNA not passed from a parent to a child, which will also alternate between grandparent streams at recombination points, but with opposite phase as the previous category)
- Child x Parent (representing the DNA inherited from the opposite parent)
However, the Ultimate Phaser can be applied to any two related individuals, resulting in unbound output. Where the two input kits include half-identical regions (HIR), the result is meaningful phased data. However, in fully identical regions (FIR) or not identical regions (NIR), the tool produces data devoid of genealogical significance, and therefore the kit must be bound prior to contributing to a reconstruction project. The toolkit allows for flexible binding, using the Extract Segments tool as a custom filter allowing user-selected thresholds via GEDmatch segment import.
Tools added in v2.0
Certain features and tools in the first release version (v1.5) of the toolkit were disabled as they were in various stages of testing and development. The first tool to be added to the kit in November, 2018, was the Imputer tool in v2.0. While the phasing engine of Borland Genetics already imputed some data to its output kits, the Imputer tool allows users to add customized segments of imputed DNA data to fill gaps in partial reconstructions. The software suggests data corresponding to missing segments in a partial reconstruction based on a user-selected confidence threshold set between 75% and 99%.
Tools added in v2.1
The Script Manager (used to develop some of the stand-alone phasing workflows) now allows users to write or record scripts for custom workflows and share them with other users. The tool was enabled in v2.1 after a simplification of script syntax.
Tools added in v3.0
In v3.0, the Creeper tool was introduced that allowed users to enter a family tree data structure representing the familial relationships between resource donors, and suggested reconstruction workflows based on available resources and family connections.
Tools added in v3.1
The Creeper functionality in the Desktop Toolkit was discontinued in v3.1 but remains a central component of the Borland Genetics Web Tools and Database. V3.1 was primarily an efficiency upgrade and contained algorithms to handle some of the newer raw data file formats. Along with the v3.1 release, the HIR Mapper, Borland Genetics' first web tool was also released. This version of the HIR Mapper used match data from the GEDmatch Segment Search output to find the boundaries between segments in phased kits and pre-populates a spreadsheet with the cousin matches on each segment in a format compatible with DNA Painter. Then, once the segments are reviewed in DNA Painter, the output can be fed to the Reverse Phase and Extract Segments tools. This version of the HIR Mapper was deprecated in 2019 in favor of a version that is better integrated with the Borland Genetics Web Tools and Database.
- Kevin Borland (USA) was the primary developer of the software.
- Leonardo Alminana (Argentina) provided assistance in low-level programming, converting the desktop toolkit into a form that could be distributed across Windows and Mac platforms. The Mac version of the software is to be released shortly pending security certificate issuance.
- Steven Borland (USA) assisted in the debugging of several key features of the desktop toolkit.
- Borland Genetics' team of 70 volunteer beta testers was vital in transitioning the desktop toolkit from a personal science lab to a commercial-grade software resource suitable for distribution among the genetic genealogy community. Testers who went above and beyond expectations providing significant indispensable input include Jason Porteous (Canada), Rusty Erpenbeck (USA) and Gonçalo Marques (Portugal).
- Borland Genetics Desktop Toolkit, direct link to a Dropbox folder from where the Windows version of the desktop software can be downloaded, along with an instruction manual and press release.