Resource Manager (Borland Genetics)

The Resource Manager is a menu option in the Borland Genetics DNA software toolkit that allows organization of raw DNA files stored in the Data Library.

Active Resource List
Any Borland Genetics workflow begins by selecting “Manage DNA Resources” from the Main Menu of options. Upon selecting “Manage DNA Resources” for the first time in any session, the Active Resource List’s contents will be empty.

Add B37 Resource
All tools in the Borland Genetics toolkit require at least one build 37 raw DNA resource in the Active Resource List. To add a single build 37 raw DNA resource to the Active Resource List, the user must select the “Add B37 resource” option from within the Research Manager. The user is then prompted via a file dialogue to locate the desired resource within the Data Library.

Only .txt or .csv raw DNA files that use build 37 human genome coordinates are compatible with the toolkit. All raw DNA files provided by Ancestry.com, 23 & Me and MyHeritage use build 37 coordinates, and are therefore compatible. FamilyTreeDNA kits are also compatible, but when prompted by FamilyTreeDNA to select an output type, the user should select “Build 37 Raw Data Concatenated” for full compatibility.

Once a build 37 DNA resource is selected from the Data Library, the user is prompted to enter the gender of the donor. This is important, as it determines how Borland Genetics tools will handle the X chromosome.

Users are also given the opportunity to enter a GEDmatch kit number, although doing so is not required. This feature is intended as a book-keeping function only, and leaving this field blank will not affect the functionality of the tools.

Naming and Renaming DNA Resource Files
DNA resources should be uniquely named before accessing them via Borland Genetics. Once a DNA resource is added to the Active Resource List, renaming the file manually using Windows Explorer may result in a fatal error or otherwise undesirable results. If a user wishes to remove one or more resources from the Active Resource List so they can be renamed, this can be done via the “Remove resource(s)” option. After renaming the resource file, the user may then use the “Add B37 resource” option to restore the resource to the Active Resource List.

When naming or renaming a DNA resource, the special characters “%” and “'” (apostrophe) and "." (period) must be avoided, as these characters within a resource name will affect the functionality of certain tools.

Reconstructed/synthetic DNA kits generated by Borland Genetics may contain the aforementioned special characters (such as to indicate reconstruction coverage percent). Users should not attempt to edit or rename automatically generated Borland Genetics output kits in the Data Library as doing so will affect the functionality of certain tools.

Removing DNA Resource Files
If you no longer wish to include one or more DNA resources in the Active Resource List, simply select the “Remove Resource(s)” option.

The most common reason to remove a resource is that a duplicate resource was accidentally added to the list or that one of the Borland Genetics tools over-wrote a previous synthetic output kit with the same name thereby creating a duplicate entry.

Another popular reason for temporarily removing a resource from the Active Resource List is so that it can be manually renamed in the Data Library using Windows Explorer. It is not recommended that users manually rename synthetic output kits created by Borland Genetics, as altering the structure of the filenames automatically generated by Borland Genetics (or inconsistent naming of the accompanying “Reconstructed Segments” file associated with a synthetic output kit) can cause a fatal error resulting in data loss.

Removing a resource from the Active Resource List does NOT delete the associated resource from the Data Library. If you wish to do so, you may delete the resource using Windows Explorer.

Understanding and Editing DNA Resource Attributes
DNA Resource attributes are listed under the column headers of the Active Resource List. Some of the attributes assigned to DNA resources will be familiar to you such as “Gender” and “GedMatch ID.” These attributes can be manually edited to correct an error or to reflect updated information, using the “Edit Resource” option. Selecting the correct gender is important as it affects the functionality of Borland Genetics tools that handle the X chromosome.

The most common use of the “Edit Resource” feature is to add a GedMatch kit number to a Borland Genetics output resource, once one has been assigned by GedMatch, so as to keep track of which versions of your reconstructions have been uploaded to GedMatch. When uploading a Borland Genetics output kit to GedMatch, you will currently be assigned a kit number beginning with the letter “Z.” IMPORTANT:  Please be sure to mark Borland Genetics kits as “research” on GedMatch unless you have confirmed that making the kit public is permitted under GedMatch terms of service. Also, when uploading a Borland Genetics kit to GedMatch, be sure to select the appropriate option designating the kit as “artificial.” Doing so will not in any way impair the kit’s ability to generate full lists of cousin matchs in GedMatch one to many tools.

Borland Genetics also assigns two attributes to raw DNA files with which you will likely be unfamiliar, i.e. “Type” and “Coverage.” These attributes cannot be edited as they are assigned or calculated by Borland Genetics based file contents. Their meaning will be discussed in greater detail on the following page.

The “Kit Name” attribute does not necessarily exactly match the Windows filename associated with a DNA resource. “Kit Name” cannot be edited from within Borland Genetics. If you wish to rename a DNA resource, please follow the instructions for naming and renaming DNA resource files, included elsewhere in these instructions.

Although “Kit Name” doesn’t always match the Windows filename, you should still easily be able to recognize the kit from its kit name in the Data Library. The version of the DNA resource suitable for GedMatch upload will be the zipped copy in the Data Library. All Borland Genetics reconstruction tools automatically provide a zipped copy in addition to ordinary output for this purpose.

Type Attribute
Humans have two copies of each autosomal and sex chromosome, one having been inherited paternally, and the other maternally.

Commercial DNA kits provide test results in raw data files with paternal and maternal readings of the bases at each tested position randomly listed in no discernable order. This is referred to as “unphased” data.

Borland Genetics uses a phasing engine to organize the contents of DNA files into a usable form. The first step of any reconstruction workflow is to apply tools to reduce all or some portions of factory DNA kits into “Mono” kits. A mono kit only contains data from one copy of each chromosome at any given position. Borland Genetics “Mono” kits are not necessarily “phased” in the traditional sense, as they may contain segments from both the paternal and maternal side, but they are organized in a way that they can be easily manipulated to reconstruct synthetic DNA kits of relatives.

In come cases, by using data from multiple donors, enough DNA can be isolated for a relative that reconstructed segments will overlap (with parts of the paternal and parts of the maternal copies reconstructed across the same span of chromosome). In this case, a “Stereo” DNA resource is required to handle the additional information.

Typically, it is best to avoid creating “Stereo” type kits until the final stage of reconstruction after all “mono” contributions to a reconstruction target are assembled from donors.

Coverage Attribute
As its name suggests, the “coverage” attribute indicates the percentage of the chromosomes covered or included in a synthetic kit or a reconstructed ancestor. The maximum coverage amount for a “Mono” kit is 50%, whereas the maximum coverage amount for a “Stereo” kit is 100% (as “Stereo” kits contain data pertaining to both copies of each chromosome).

When a “Mono” kit achieves full 50% coverage (such as in parent/child phasing), it is referred to as “full.” Likewise factory kits from test providers are generally full “Stereo” kits (with the exception of some FamilyTreeDNA kits missing the X chromosome.

In these instructions, you will see the terms “clade” and “contributor” used to denote certain donors to a reconstruction project. The difference relates to the maximum amount of coverage obtainable by combining data from individual donors. By combining DNA of contributors within a clade, the maximum achievable coverage is 50% (representing the DNA of top member of the clade inherited from whichever of his or her parents is the target of reconstruction). However, when data across clades is combined, the maximum coverage is 100%, as different sibling clades will have inherited different portions of the target’s DNA. Handling data within a clade should be done entirely with mono tools (including merges). Handling data across sibling clades must be one with stereo tools (such as merging one or more cross-clade mono kits to a single stereo kit).

Saved Resource Lists
In addition to adding individual resources one by one to the Active List, you can also save and load entire lists of DNA resources from and to the Active Resource List. You can think of this as the functional equivalent of subdirectories or subgroupings of your DNA resources by project. Simply choose the “Load Resource List” and/or “Save Resource List” options. Resource lists are saved in the Data Library, and can be renamed manually in Windows Explorer as long as the list is not currently loaded to the Active Resource List. Upon close of the program, or before opening a new resource list from the Data Library, you will be prompted to save your Active Resource List if any changes have been made.