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INBUPGF90

INBUPGF90 is a program to calulate inbreeding coefficients.

Written by Ignacio Aguilar & Ignacy Misztal, 06/2006 - 08/2012

Instituto Nacional de Investigacion Agropecuaria, Uruguay
University of Georgia, US

Summary

This program calculate inbreeding coefficients using a recursive algorithm assuming non-zero inbreeding for unknown parents as presented in Aguilar & Misztal 2008, JDS 91:1669-1672.
The methodology to calculate inbreeding accounting for missing parents is based on VanRaden, 1992.

Pedigree files not need to be in a particular order.
Alphanumeric identification of individuals are supported, with a default length of 20 characters (see below to change it).

Pedigree file should contain information for Individual Id, Sire Id and Dam Id.
Year of birth is not required to calculate inbreeding coefficients, but inbreeding for individuals with missing parents wont be calculated if year of birth is not provided.

Usage

inbupgf90 --pedfile <file_name>  [ ... ]

pedfile is assumed to have 3 fields with identification for animal, sire and dam, separated by at least one space.
Missing sire or dam identification should be coded as '0', but in case of reading with fixed format (see below) blank spaces are supported.
Individuals with missing sire and dam are not required to be listed in the pedigree file.

Optional command arguments

--alpha_size <n>

change the maximun length of characters for alphanumeric Ids.

--fmt <fmt>

to read pedigree file with fixed format. Variables are assumed to be alphanumeric, e.g. '(3a8)'

--yob

indicate that year of birth should be read in the 4th column.
Checks based on year or birth will be performed between the individual and their parents.
Non-zero inbreeding for animals with missing parents could be calculated if more than one iteration is used (see niter)

--ngen <n>

Indicate the generation interval to assign missing year of birth.
default 3

--mngen <n>

Indicate the generation interval to check parents
default 0

--niter <n>

specify maximun number of iterations to assign non-zero inbreeding for individuals with missing parents. default is 1 i.e. zero inbreeding for individuals with missing parents.

--method <n>

Several methods can be used:
1 - recursive as in Aguilar & Misztal, 2008 (default)
2 - recursive but with coefficients store in memory, faster with large number of generations but more memory requirements
3 - method as in Meuwissen & Luo 1992

Misc

--prnrenped

using this option the renumber pedigree (parents Id precede their progeny Id) will be printed to a file.
Inbreeding coefficients are not calculated !!!

Calculation of inbreeding and relationship coefficients for specific animals/matings

Calculations of future inbreeding for potential matings or for specific list of animals could be achived using the following command arguments.
Two files should be provided sfile and dfile, with nsire and ndam rows respectively.
All relationship between nsire with ndam will be computed. Only inbreeding for required animals will be calculated!!

--sfile <SireFile>

indicate the name of a file that contains a list of nsire individuals to be used as 'sires'

--dfile <DamFile>

indicate the name of a file that contains a list of ndam individuals to be used as 'dams'

--nrmcoeff

the matrix of relationship information between nsire*ndam with printed out in a file “SireFile_DamFile.nrmcoeff” format of file is sireId, damId, relationship coefficient

--matings

for each dam the sire that results in a mating with the minimun inbreeding is listed as well as the inbreeding resulting from the other sires. format of file is DamId, SIreWithMinimunInb,SireID1….SireIDn

--allped 

Perform calculation of inbreeding coefficients for all individuals.

--nrmcoeff_list <ListFile>

statistics of relationship information between all individuals in ListFile were calculated and printed out in a file “ListFile.nrmcoeff” format of file is Id_i, Id_j, relationship coefficient

Example

The following example is based on the pedigree provided by Emik & Terril, 1949. J. Hered. 40:51–55, modified with year of birth information.

Here code for missing sire/dam is space, so fixed format is need to read the file properly !!!!

Pedigree file: pedet

1646RW  619RW   719RW   99 
619RW   3340R   2475R   96 
719RW   438WP   3840R   96 
3840R   3340R   2695R   92 
3340R   2220R   2320R   91 
2220R   823R    1277R   87 
2695R   823R    1475R   80 
2320R   823R    1829R   85 
1277R   382R            83  
1475R   823R    1072R   73 
1829R   823R    1338R   81  
2475R   823R    1052R   92   
382R    3180R           79         
1072R   164R            69  
823R    59R     218R    68 
1338R   67R     368R    78  
1052R   K4465           85     
368R    K4465           75  
67R     LOWE6           70  
59R     LOWE6           65   
164R    LOWE6           65      
3180R   LOWE6           75

Using INBUPGF90 to get regular inbreding coefficients

Command

inbupgf90 --pedfile pedet --fmt '(3a8)'

Log output

 Options
    --pedfile pedet
    --fmt (3a8,a3)

 Fields to read:  animal, sire, dam

 Maximum length for alphanumeric fields: 20

 Ordering will be performed by: Parents with relationships first
 table expanded from           37  to           74  records

 Elapsed time for reading and hash: .002

 Pedigree file "pedet": 22 records

 Total number of animals in pedigre: 26

 Elapsed time after checks:  0.149E-03

 Elapsed time for renumber using Parent First:  0.200E-05

 Calculating Inbreeding coefficients with Recursive method 

 Round: 1 elapsed time:  0.11000E-04
 Average inbreeding (%):    5.26921 - # of animals: 26

 Distribution of animals by inbreeding coefficients

 Inbreeding (%) class        N       %
 -------------------------------------
              =  0.00       17   65.38
         0.00 -  6.25        3   11.54
         6.25 - 12.50        0    0.00
        12.25 - 18.75        2    7.69
        18.75 - 25.00        2    7.69
              > 25.00        2    7.69

 Creating output file: pedet.solinb  

Inbreeding coefficients file: pedet.solinb

2695R                 0.2656250
218R                  0.0000000
719RW                 0.0000000
3840R                 0.2470703
67R                   0.0000000
1646RW                0.1502686
1475R                 0.0312500
382R                  0.0000000
59R                   0.0000000
3340R                 0.1992188
1277R                 0.0000000
368R                  0.0000000
LOWE6                 0.0000000
823R                  0.0000000
619RW                 0.1640625
164R                  0.0000000
438WP                 0.0000000
1829R                 0.0312500
2475R                 0.0000000
2220R                 0.0156250
1338R                 0.0000000
1072R                 0.0000000
1052R                 0.0000000
2320R                 0.2656250
3180R                 0.0000000
K4465                 0.0000000

Using INBUPGF90 to get inbreeding coefficients assuming nonzero inbreeding of unknown parents

inbupgf90 --pedfile pedet --fmt '(3a8,a3)' --yob --niter 10 

Log output

 Options
    --pedfile pedet
    --niter 10
    --yob
    --fmt (3a8,a3)

 Fields to read:  animal, sire, dam ,yob

 Maximum length for alphanumeric fields: 20

 Ordering will be performed by: Year of Birth
 table expanded from           37  to           74  records

 Elapsed time for reading and hash: .003

 Pedigree file "pedet": 22 records

 Total number of animals in pedigre: 26

 Min YOB: 62 - Max YOB: 99

 Elapsed time after checks:  0.226E-03

 Calculating Inbreeding coefficients with Recursive method  based on: YOB

 Round: 1 elapsed time:  0.190E-04 convergence:  0.52692E-01
 Average inbreeding (%):    5.26921  # of  animals:         26

 Round: 2 elapsed time:  0.170E-04 convergence:  0.18517E-01
 Average inbreeding (%):    7.12092  # of  animals:         26

 Round: 3 elapsed time:  0.130E-04 convergence:   0.0000    
 Average inbreeding (%):    7.12092  # of  animals:         26

 Average inbreeding (%) by YOB

 code   num_anim    avg_inb
 --------------------------
   62          1      0.000
   63          0      0.000
   64          0      0.000
   65          3      0.000
   66          0      0.000
   67          0      0.000
   68          1      0.000
   69          1      0.000
   70          1      0.000
   71          0      0.000
   72          1      0.000
   73          1      3.125
   74          0      0.000
   75          2      0.000
   76          0      0.000
   77          0      0.000
   78          1      0.000
   79          1      0.000
   80          1     26.562
   81          1      3.125
   82          0      0.000
   83          1      0.000
   84          0      0.000
   85          2     13.281
   86          0      0.000
   87          1      1.562
   88          0      0.000
   89          0      0.000
   90          0      0.000
   91          1     19.922
   92          2     18.994
   93          1      0.000
   94          0      0.000
   95          0      0.000
   96          2     11.523
   97          0      0.000
   98          0      0.000
   99          1     16.687

 Distribution of animals by inbreeding coefficients

 Inbreeding (%) class        N       %
 -------------------------------------
              =  0.00       15   57.69
         0.00 -  6.25        3   11.54
         6.25 - 12.50        0    0.00
        12.25 - 18.75        2    7.69
        18.75 - 25.00        3   11.54
              > 25.00        3   11.54

 Creating output file: pedet.solinb 
   

Inbreeding coefficients file: pedet.solinb

2695R                 0.2656250
218R                  0.0000000
719RW                 0.0000000
3840R                 0.2470703
67R                   0.0000000
1646RW                0.1668701
1475R                 0.0312500
382R                  0.0000000
59R                   0.0000000
3340R                 0.1992188
1277R                 0.0000000
368R                  0.0000000
LOWE6                 0.0000000
823R                  0.0000000
619RW                 0.2304688
164R                  0.0000000
438WP                 0.0000000
1829R                 0.0312500
2475R                 0.1328125
2220R                 0.0156250
1338R                 0.0000000
1072R                 0.0000000
1052R                 0.2656250
2320R                 0.2656250
3180R                 0.0000000
K4465                 0.0000000
readme.inbupgf90.1413988676.txt.gz · Last modified: 2014/10/22 14:37 by ignacio