Input File Handling:

This software requires an input file for each breeding colony to be analyzed. Multiple separate pedigrees within the same breeding colony can be accommodated within the same input file.
If an animal is missing information on one parent, that cell should be blank. For animals with no information on either parent, both cells under "Sire ID" and "Dam ID" should be blank. For animals with information on one parent a unique "placeholder" ID will be made up by the software to represent the unknown parent. Placeholder IDs are marked TRUE in the placeholder column and appear on the Pedigree Browser tab when "Display Unknown IDs" is checked. Please be aware that animals with no parents will be treated as founders in these calculations, i.e., sources of new genetic variation in the colony.
An empty cell in any column is read as missing information, the same as "NA": a blank parent is an unknown parent, a blank ancestry is read as UNKNOWN, and a blank origin means no origin was recorded.
Genotypic information for a single locus can be included in the genetic analyses. See Pedigree File Format and Genotype File Format below for file descriptions. Observed genotypic information can be supplied for any members of the pedigree. Designation of two alleles is required as currently there is no accommodation for partial genetic information for an individual. Please contact R. Mark Sharp if you need to be able to enter partial genetic information.

Pedigree File Format Details:

The following columns names are reserved and will be recognized:

Ego ID, Sire ID, Dam ID, Sex, and Birth are required columns. The Birth column must be present, but its values may be blank when an Age column is supplied.

Use the Allowable Names listed in the table below. Allowable Name case and order are not significant. The first Allowable Name listed for each column is the name used internally and is the name used in examples and output.
Ego ID, Sire ID, and Dam ID values must not contain a period ("."); a period in an ID is not allowed and is rejected during quality control. Periods cause problems across software environments (column-name and formula parsing in R, file-name extensions, programming-language namespaces, and regular expressions). This rule is enforced when data are read in (qcStudbook) and is honored by all automatically generated IDs.
If the Age column is provided, the program will use the user-specified age.
Otherwise, the program will calculate age based on the Birth column and the current date, or the Death, Departure, or Exit columns, if provided.
Exit dates, if provided, will supercede Death and Departure dates. If Exit is not provided, Death and Departure will be combined based on which date is chronologically first. (This functions primarily to catch clerical errors or historical changes in record-keeping practices).
Dates should be in the format YYYY-MM-DD (this date option can be found under the "English-U.K." locale option under the "Format Cells -> Number -> Date" menu in Excel 2010).
Genotype data may be supplied within the pedigree file or in a separate genotype file (described below). In a one-file pedigree the two allele columns can be named first and second, first_name and second_name, or allele_1 and allele_2, and can hold whole numbers or text labels such as A, B, C, which become whole-number codes the same way as in a separate genotype file. After Read and Check Pedigree the QC Summary says which columns were read, how many different alleles it found and for how many animals, so a misspelled label shows as one extra allele; for example, "Genotypes read from allele1 and allele2: 3 different alleles (A, B, C) for 8 of 8 animals." When no usable pair of columns is found it says so instead: a line that begins "No genotype columns were found" and names the column names it looked for, or, when columns were found that are not a usable pair, one that begins "Genotype columns were found" and names them.

Allowable Name	Description of Information	Data Format
id, egoid, ego_id	Ego ID: Unique animal identifier	Text with no period (".")
sire, sireid, sire_id	Sire ID: Unique identifier of the ego's father	Text with no period (".")
dam, damid, dam_id	Dam ID: Unique identifier of the ego's mother	Text with no period (".")
sex	Sex: Ego's sex	Sex can be indicated by any of the following: Male: ("male", "m", "1"), Female: ("female", "f", "2"), Unknown: ("unknown", "u", "3") Case and spaces around a code are ignored. A blank, hermaphrodite ("hermaphrodite", "h", "4") or other unrecognized value is read as Unknown.
age	Age: Age at exit, or current age of the ego (optional).	Age in decimal years
birth, birthdate, birth_date	Birth: Ego's date of birth (required column)	YYYY-MM-DD Format
death	Death: Ego's date of death	YYYY-MM-DD Format
departure	Departure: Ego's date of sale	YYYY-MM-DD Format
exit	Exit: Ego's date of exit from the colony. (Supercedes Death or Departure information)	YYYY-MM-DD Format
name	Name: Ego's human-readable name or nickname (optional). Not every center records this, and not every animal needs one -- shown alongside id on the Pedigree Diagram tab when the "Show Names on Diagram" option is enabled, and removed by the de-identification (obfuscation) workflow.	Free text
first	First allele: the animal's first allele	Whole numbers or text labels.
second	Second allele: the animal's second allele	Whole numbers or text labels.

Upload an Excel file (.xlsx or .xls) or a text file (.csv or .txt). Choose the matching "File Type" (Excel is the default); for a text file also choose its separator (comma, semicolon or tab). A spreadsheet can be saved as a "tab-delimited" or "comma-delimited" text file with the "Save As" function in Excel.
Select the correct file type and file content, click on "Select Pedigree File" (or the file button that appears for the content you chose) to choose the file, and then click on "Read and Check Pedigree".
The pedigree information displayed in the Pedigree Browser will not appear exactly the same as the input file. The pedigree shown in the Pedigree Browser has been built using input file contents that may be used to produce other columns of information displayed. Input file processing will include:
- A check for the 5 required fields: Ego ID, Sire ID, Dam ID, Sex, and Birth.
- A new row entry will be added for any Sire or Dam that do not already have their own row as an Ego.
- Animals will be checked to ensure that their sex is consistent throughout the file.
- Duplicate rows will be removed.
- If Death or Departure date columns have been included, an "Exit" column will be built. Otherwise, Exit date assignment will be skipped if an Exit date column was provided in the input file.
- If Birth dates have been included, age will be calculated as (Exit Date - Birth Date) / 365.25, rounded to 0.1 year. If an animal has no Death, Departure, or Exit date, it is assumed to be still alive and Age will be calculated as (Today's Date - Birth Date) / 365.25. Age calculation will be skipped if an Age information column is included in the input file.
- Generation numbers will be added to each ego.
- Families (Pedigrees) will be numbered and this information will be added to each ego.

Genotype File Format Details:

The following columns names are reserved and will be recognized:

The genotype file needs at least three columns: the ID column first, then the two allele columns, which are read by position, so their names may be anything except first and second (first_name and second_name are the conventional names).

Columns first and second will be automatically generated and cannot be present.

Use the Allowable Names listed in the table below. Allowable Name case and order are not significant. The Allowable Name listed for each column is the name used internally and is the name used in examples and output.
Genotype data can be supplied within the pedigree file or in this genotype file. Only two additional columns (first and second) are required when the genotypes are provided within the pedigree file. See table above for a description. The genotype file columns are described below.

Allowable Name	Description of Information	Data Format
id (first column)	ID: Unique animal identifier	Alphanumeric characters (no symbols, including no period ".")
first_name (second column)	Allele 1: Alphanumeric representation of first allele	Currently limited to alphanumeric values, underscores, spaces and dashes. Other characters have not been tested.
second_name (third column)	Allele 2: Alphanumeric representation of second allele	Currently limited to alphanumeric values, underscores, spaces and dashes. Other characters have not been tested.

The genotype file can be an Excel file (.xlsx or .xls) or a text file (.csv or .txt), using the same File Type and separator choices as the pedigree file.
Choose "Pedigree(s) and genotypes in separate files" as the File Content, click on "Select Genotype File" to choose the file, and then click on "Read and Check Pedigree".