rtahmasbi / Kinship

Calculate Kinship matrix

Kinship

Calculate Kinship matrix

Download

git clone https://github.com/rtahmasbi/Kinship

Compile

make

Examples

Example 1

In this example, all the individuals are in one file.

kinship --file_pedigree pedigree1.txt --out test1

Example 2

You can also calculate kinship from different generation files. For example, to calculate kinship form GeneEvolve output info files for the last 6 generations (generations 5 to 10), you can run the following commands:

# step 1: create a list file for pedigree info:
rm file_pedigree_list.txt; 
for i in $(seq 5 10); do echo -e out1.info.pop1.gen$i.txt >> file_pedigree_list.txt; done
# step 2: run kinship
kinship --file_pedigree_list file_pedigree_list.txt

For more info on GeneEvolve, please check https://github.com/rtahmasbi/GeneEvolve.