fixped.f90	Checks pedigree relationships and discovers additional relatives
Downloads	Program files and executable
Input	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 animals
	clone.keys	Links known identical animals to one member of clone group
	For 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 animals
	hap.listpriors	hap.list from a prior full run
	hap.foundpriors	hap.found from a prior full run
	hap.filledpriors	hap.filled from a prior full run
Steps	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 ¾ sibs Output discovered dam if unknown but full sib has a dam Discover dam and clones if neither sire nor MGS are genotyped
Output	bestmatches	Ancestor type: MGS, MGGS
		Dam/maternal grandam (MGD) source codes:
		0	Unknown (no identification information)
		G	Genotyped
		I	Imputed
		P	Pedigree dam or MGD of genotyped animal (has identification information but not genotyped)
		Match:
		0	No likely MGS/MGGS found to replace unknown
		1	Pedigree MGS/MGGS has most matches
		2	Pedigree MGS/MGGS has 2nd most matches
		3	Pedigree MGS/MGGS has 3rd most matches
		4+	Pedigree MGS/MGGS has 3 or more bulls with more matches
		ADD	Add MGS/MGGS replacing missing
		DEL	Pedigree MGS/MGGS is unlikely, no better candidate found
		FIX	MGS/MGGS found, likely the true ancestor to replace genotyped one
		P	Pedigree MGS/MGGS not genotyped
		SUB	MGS/MGGS found, likely the true ancestor to replace nongenotyped one
	bestmatchesEXTRA	Ancestor type: Dams, sires, full sibs, PGS, clones
		Relative type:
		CLON	Identical genotype
		DAM1	Check and confirm if dam genotyped or delete if low match
		DAM2	Output discovered dam if unknown but full sib has a dam
		DAM3	Output discovered dam among daughters of MGS
		DAM4	Discover dam and clones if neither sire nor MGS are genotyped
		SIRE	Sire
		FSIB	Full sib
		PGS	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 not
		LOW	Reported sire has low number of matches; no better match found
References	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 Laboratory
 Agricultural Research Service, USDA