U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Animal Genomics and Improvement Laboratory: Beltsville, MD
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                                    Software
                People

                    Staff Listing
                                    Careers


        


                    AIP
                        Home
                                    About
                                    Publications
                                    Software
                                    People
                                    Collaborations
                                    Careers
                                    Centennial
                                    Contact
                                    Dairy industry links
                    DirectionsSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Genomics and Improvement Laboratory AIP Software





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications
- Home
- About
- Publications
- Software
- BESTPRED
- ConvertCufflinksToExcel
- FINDHAP
- FINDMAP
- FIXPED
- GENOSIM
- MTDFREML
- MTGSAM
- People
- Collaborations
- Careers
- Centennial
- Contact
- Dairy industry links
- Home
- Queries login
- News
- Animal Evaluation lists
- Genotype counts

**fixped.f90**
Checks pedigree relationships and discovers additional relativesDownloads
Program files and executableInput
Mostly the output files from findhap, version 3. Other input files are:pedigree.file
Contains genotyped animals and their ancestors (same file used in findhap)Provides a more complete file than just known ancestors of genotyped animals.../pedigrees.txt
Provides a more complete file than just known ancestors of genotyped animalsclone.keys
Links known identical animals to one member of clone groupFor faster processing, input files from findhap can include only new animals and then link to the following full files from findhap that included all prior animals:pedigree.priors
Same format as pedigree.file but for all prior animalshap.listpriors
hap.list from a prior full runhap.foundpriors
hap.found from a prior full runhap.filledpriors
hap.filled from a prior full runSteps
Confirm if genotyped sire matches
Remove confirmed sire haplotypes from animal
Check and confirm if dam genotyped
Confirm if genotyped dam matches
Check maternal sibs for clones, full sibs
Confirm if genotyped maternal grandsire (MGS) matches
Search for MGS, paternal grandsire (PGS), or sire if needed
Remove confirmed or found MGS haplotypes from animal
Search for maternal great-grandsire (MGGS)
Check among paternal sibs for clones, full sibs. If MGS known, restrict search to 3⁄4 sibs
Output discovered dam if unknown but full sib has a dam
Discover dam and clones if neither sire nor MGS are genotypedOutput
bestmatches
Ancestor type: MGS, MGGSDam/maternal grandam (MGD) source codes:0
Unknown (no identification information)G
GenotypedI
ImputedP
Pedigree dam or MGD of genotyped animal (has identification information but not genotyped)Match:0
No likely MGS/MGGS found to replace unknown1
Pedigree MGS/MGGS has most matches2
Pedigree MGS/MGGS has 2nd most matches3
Pedigree MGS/MGGS has 3rd most matches4+
Pedigree MGS/MGGS has 3 or more bulls with more matchesADD
Add MGS/MGGS replacing missingDEL
Pedigree MGS/MGGS is unlikely, no better candidate foundFIX
MGS/MGGS found, likely the true ancestor to replace genotyped oneP
Pedigree MGS/MGGS not genotypedSUB
MGS/MGGS found, likely the true ancestor to replace nongenotyped onebestmatchesEXTRA
Ancestor type: Dams, sires, full sibs, PGS, clonesRelative type:CLON
Identical genotypeDAM1
Check and confirm if dam genotyped or delete if low matchDAM2
Output discovered dam if unknown but full sib has a damDAM3
Output discovered dam among daughters of MGSDAM4
Discover dam and clones if neither sire nor MGS are genotypedSIRE
SireFSIB
Full sibPGS
Paternal grandsire (top 3 listed may also include MGS)Match:OK
Haplotypes confirm pedigree (used with CLON and FSIB)SUG
Discovered full sib has pedigree dam, but this full sib does notLOW
Reported sire has low number of matches; no better match foundReferences
2020
Nani, J.P., L.R. Bacheller, J.B. Cole, and P.M. VanRaden. Discovering ancestors and connecting relatives in large genomic databases. J. Dairy Sci. 103:1729–1734.2013
VanRaden, P.M., T.A. Cooper, G.R. Wiggans, J.R. O'Connell, and L.R. Bacheller. Confirmation and discovery of maternal grandsires and great-grandsires in dairy cattle. J. Dairy Sci. 96:1874–1879.License
Fortran package fixped is public domain and was developed with U.S. taxpayer funding. Accurate results are not guaranteed. Please report any bugs to juanonani@gmail.com. You may modify, improve, use, and redistribute the code to anyone for any purpose. Or, you can ask Juan to make changes that could benefit U.S. evaluations and other users. **Juan Nani****Paul VanRaden**Animal Genomics and Improvement LaboratoryAgricultural Research Service, USDA


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov