Data preparation with RENUMF90

Yutaka Masuda

September 2019

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Genomic model with SNP-marker file

Required files

Single-step GBLUP (ssGBLUP) model is an extension to the animal model. RENUMF90 can handle ssGBLUP using a similar parameter file to the animal model with an additional option. Let us use the previous files. The following files are the same as the previous ones with different names.

  ID006  A  1  1.0  3.0
  ID009  A  2  1.0  2.0
  ID012  A  1  2.0  4.0
  ID007  B  2  2.0  6.0
  ID010  B  1  1.0  3.0
  ID013  B  2  2.0  6.0
  ID008  C  1  2.0  6.0
  ID011  C  2  1.0  6.0
  ID014  C  1  1.0  8.0
  ID015  C  2  2.0  4.0

The pedigree file is as follows.

 ID001      0      0
 ID002      0      0
 ID003      0      0
 ID004      0      0
 ID005      0      0
 ID006      0      0
 ID007  ID002  ID005
 ID008  ID001  ID004
 ID009  ID002  ID003
 ID010  ID007  ID006
 ID011  ID007  ID004
 ID012  ID011  ID008
 ID013  ID011  ID010
 ID014  ID009  ID013
 ID015  ID011  ID010

An SNP-marker file should be prepared as a fixed-length text file with 2 columns: the original ID for column 1 and genotypes for column 2. See the previous chapter for the detailed explanation about the marker-file format. We use the same file shown before.

ID002 1212020111001211212000102001202022201112000110020102011001012212110122100001210101112200210010022220
ID004 2222020200110122210121001100022221102111000010011202020002002222000222000020120000020200200000200220
ID006 2122020101100221121111212100112111112212000101012211111001201211112022100201220110022200220020111120
ID010 2111121101111210121211112210202021211211000110021211111001101211101122100111221000022200120020101120
ID011 2211121200121111220211011210112121111201000120011202020002002222000222000021221000021200110010101220
ID012 2222020200110122210121001100022221102111000010011202020002002222000222000020120000020200200000200220
ID013 2122020101210121121222101200112122102212000010012211111001101211101122100110220000021200210010200120
ID015 2122020101210121121222101200112122102212000010012211111001101211101122100110220000021200210010200120

The marker file is never altered and duplicated by RENUMF90. The program just read the 1st column (the original ID) and make a table relating the renumbered animal ID to the original animal ID. The table will be saved as a cross-reference file.

We assume the same animal model described before except that the genomic information is included. The following is a parameter file to handle the SNP file.

DATAFILE
rawdata4.txt
TRAITS
5
FIELDS_PASSED TO OUTPUT

WEIGHT(S)

RESIDUAL_VARIANCE
2.0
EFFECT           # 1st effect fixed
2 cross alpha
EFFECT           # 2nd effect fixed
3 cross alpha
EFFECT           # 3rd effect fixed
4 cov
EFFECT           # 4th effect
1 cross alpha
RANDOM           ## treated as a random effect
animal
FILE             ## pedigree file
rawpedigree4.txt
FILE_POS         ## animal, sire and dam IDs with two 0s
1 2 3 0 0
SNP_FILE         ## SNP marker file
snp4.txt
(CO)VARIANCES    ## its variance component
0.5

A new keyword SNP_FILE with the name of marker file tells RENUMF90 to properly treat the marker file. This keyword should be placed just after FILE_POS.

Renumbered files

Running RENUMF90 with the above instruction, it generates several files in the same folder (directory). With this example, RENUMF90 will generate 5 files: renf90.dat, renf90.par, renf90.tables, renadd04.ped, and snp4.txt_XrefID. The last one is the cross-reference file (or simply, the XrefID file), which contains 2 columns for the renumbered ID and the original ID as follows.

11 ID002
12 ID004
2 ID006
5 ID010
7 ID011
8 ID012
9 ID013
1 ID015

The order of genotyped animal is the same as the marker file. The name of this file is automatically determined and fixed as the original SNP file-name plus _XrefID, e.g., snp.txt_XrefID for a marker file snp.txt. You can’t change the file name.

The renumbered parameter file renf90.par looks similar as before except the option found in the last line.

OPTION SNP_file snp4.txt

The parameter file doesn’t refer to the cross-reference file because, by default, BLUPF90 programs read the standard XrefID file (SNP file name + XrefID). Usually, you don’t have to change the name of cross-reference file, so you just keep this option line. If you do rename the XrefID file, you have to add the XrefID file name to the option-line by hand (as shown in the quick tour).

The renumbered pedigree is different from the previous one.

1 7 5 1 0 12 1 0 0 ID015
12 0 0 3 0 10 0 0 2 ID004
13 0 0 3 0 0 0 0 1 ID005
2 0 0 3 0 10 1 0 1 ID006
3 11 13 1 0 2 1 2 0 ID007
4 14 12 1 0 2 1 0 1 ID008
5 3 2 1 0 12 1 0 2 ID010
6 11 15 1 0 2 1 1 0 ID009
7 3 12 1 0 12 1 3 0 ID011
8 7 4 1 0 12 1 0 0 ID012
14 0 0 3 0 0 0 1 0 ID001
9 7 5 1 0 12 1 0 1 ID013
11 0 0 3 0 10 0 2 0 ID002
10 6 9 1 0 2 1 0 0 ID014
15 0 0 3 0 0 0 0 1 ID003

With genomics, RENUMF90 assigns new integer values to animals with the following rules.

  1. First, the program assigns the smallest numbers to animals with the record(s). The order of assigned numbers will be random (i.e., not following the order found in the data file).
  2. Secondly, the program assigns the larger numbers to genotyped animals. The order will be random (i.e., not following the order found in the marker file).
  3. Lastly, the program assigns the larger numbers to animals found only in pedigree. The order will be random (i.e., not be sorted in any way).

You can find the genotyped animals in the renumbered pedigree file. When an animal is genotyped, the 6th column will be 10 or larger.

Summary

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