#### 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 (designated as UnkownID and UnkID in Pedigree Brower tab) will be assigned by the software to represent the unknown parent. 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.
- 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, and Sex are required columns.

Either Age or Birth must also be provided.

- 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 be alphanumeric with no symbols. In particular, a period (".") is not allowed in an ID 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. Only two additional columns (first and second) are required when the genotypes are provided within the pedigree file. The columns are described below.

Allowable Name | Description of Information | Data Format
--- | --- | ---
id, egoid, ego_id | Ego ID: Unique animal identifier | Alphanumeric characters (no symbols, including no period ".")
sire, sireid, sire_id | Sire ID: Unique identifier of the ego's father | Alphanumeric characters (no symbols, including no period ".")
dam, damid, dam_id | Dam ID: Unique identifier of the ego's mother | Alphanumeric characters (no symbols, including 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"), Hermaphrodite: ("hermaphrodite", "h", "4")
age | Age: Age at exit, or current age of the ego. | Age in decimal years
birth, birthdate, birth_date | Birth: Ego's date of birth | 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
allele_1 | Allele 1: Alphanumeric representation of first allele | Currently limited to alphanumeric values, underscores, spaces and dashes. Other characters have not been tested.
allele_2 | Allele 2: Alphanumeric representation of second allele | Currently limited to alphanumeric values, underscores, spaces and dashes. Other characters have not been tested.

- You will need to save your input file as a plain text file (either .txt or .csv), in order to upload it correctly. To do this, you may use the "Save As" function in Excel to save a spreadsheet in a "tab-delimited" or "comma-delimited" file format.
- Select the correct file type, and then click on "Select Input File" to upload the file.
- 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 4 required fields: Ego ID, Sire ID, Dam ID, and Sex.
  - A check for either Age or Birth information.
  - 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 (Birth Date - Exit Date) / 365.25. If no Death, Departure, or Exit dates are provided, it is assumed that the ego is still alive, and Age will be calculated as (Birth Date - Today's 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:

Columns id, first_name, and second_name are required columns.

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 | ID: Unique animal identifier | Alphanumeric characters (no symbols, including no period ".")
allele_1 | Allele 1: Alphanumeric representation of first allele | Currently limited to alphanumeric values, underscores, spaces and dashes.
allele_2 | Allele 2: Alphanumeric representation of second allele | Currently limited to alphanumeric values, underscores, spaces and dashes. Other characters have not been tested.

- You will need to save your genotype file as a plain text file (either .txt or .csv), in order to upload it correctly. To do this, you may use the "Save As" function in Excel to save a spreadsheet in a "tab-delimited" or "comma-delimited" file format.
- Select the correct file type, and then click on "Select Genotype File" to upload the file.