Script for greedily remove related samples
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GreedyRelated
LICENSE
Makefile
README.md
main.cpp
main.o
misc.cpp
misc.hpp
misc.o

README.md

Relatedness-Filtering

Script for greedily remove related samples

Installation

g++ -std=c++11 main.cpp misc.cpp -o greedy_related

Instruction

You can just type

greedy_related -h

To get all the instructions

To use with plink relatedness file, you can use the following awk script

awk -v NUM=1 'NR==1{print $2" "$4" "$10} NR!=1{print $2" "NUM" "$10; print $4" "NUM" "$10; NUM=NUM+1}'

Please note that greedy_related assume the input has a header line

Future development

  • we hope to support plink format
  • might be more tolerate with the header line?

Citation

The DOI of this software is DOI

Side Note

You can also use the --grm-cutoff function from plink if you haven't already got the relatedness information or if you don't require the phenotype aware selection