DEBV_calculator

1. A short description

• The DEBV_calculator is a module for deregressing estimated breeding values (DEBV) based on two former popular methods (Garrick et al. 2009; VanRaden et al. 2009) in Linux. The source codes of this module were written in python (by employing pandas, numpy, argparse, time, and sys libraries), and bundled using pyinstaller (https://www.pyinstaller.org/).

1.2 For downloading this modules use 'wget' command for these links:

https://github.com/Siavash-cloud/DEBV_calculator/releases/download/1.00/DEBV_calculator

https://github.com/Siavash-cloud/DEBV_calculator/releases/download/1.00/DEBV_calculator_blupf90

then run:

chmod 775 DEBV_calculator

chmod 775 DEBV_calculator_blupf90

For downloading this example datasets use this command in your Linux terminal:

git clone https://github.com/Siavash-cloud/DEBV_calculator.git

2. Inputs and usage

2.1. Type 1 (our defined format using DEBV_calculator)

2.1.1. Input

The input header must be named exactly like this:

ID	dam.ID	sire.ID	EBV.Progeny	sire.EBV	dam.EBV	PA	sire.ebv.rel	dam.ebv.rel	progeny.ebv.rel	PA.rel
5	3	1	-2.25	-3.81	-1.83	-2.82	0.86	0.58	0.73	0.73
6	3	1	-3.14	-3.81	-1.83	-2.82	0.86	0.58	0.48	0.73
7	4	5	1.79	-0.79	-2.00	-1.39	0.69	0.50	0.45	0.73

2.1.2 Usage

"./DEBV_calculator --i Data.txt --h2 0.25 --c 0.5 --o DEBV.txt"

Argument	Description
--i	input path
--h2	heritability (0<h2<1)
--c	fraction of genetic variance not explained by markers
--o	output path

2.2. Type 2 (using blupf90 outputs and DEBV_calculator_blupf90)

2.2.1. Input and usage

In the first step, you must remove the header of blupf90 solutions file using: "sed '1d' solutions > solutions2"

Note: The standard errors must have been included in your blupf90 solutions through "OPTION sol se" command in blupf90.

Then, run this command:

"./DEBV_calculator_blupf90 --s solutions2 --op Original-ped.txt --rp renadd03.ped --rt 1 --re 3 --h2 0.25 --va 18 --c 0.5 --o DEBV.txt"

Argument	Description
--s	solutions path
--op	original pedigree path
--rp	recoded (blup90) pedigree path
--rt	renumbred trait (in blup90 solutions file)
--re	renumbred effect (in blup90 solutions file)
--h2	heritability (0<h2<1)
--va	additive variance
--c	fraction of genetic variance not explained by markers
--o	output path

References

Garrick, D.J., Taylor, J.F., and Fernando, R.L. 2009. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genetics Selection Evolution 41(1): 55.

VanRaden, P., Van Tassell, C., Wiggans, G., Sonstegard, T., Schnabel, R., Taylor, J., and Schenkel, F. 2009. Invited review: Reliability of genomic predictions for North American Holstein bulls. Journal of dairy science 92(1): 16-24.