G2P

A Genome-Wide-Association-Study Simulation Tool for Genotype Simulation, Phenotype Simulation, and Power Evaluation

<p align="center"> <a href="https://raw.githubusercontent.com/XiaoleiLiuBio/G2P/master/results/G2P_logo.png"> <img src="results/G2P_logo.png" height="250px" width="450px"> </a> </p>

More abundant simulation functions could be referred to our newly developed package SIMER for simulation of life science and breeding

Authors:

You Tang and Xiaolei Liu

Contact:

[xiaoleiliu@mail.hzau.edu.cn](Xiaolei Liu)

Contents

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• Installation
  • Environment Setup
  • Windows
  • MAC
  • Linux
• Data Preparation
  • ped
  • map
  • pop
• Genotype Simulation
  • Single Population _ GUI
  • Single Population _ Pipeline
  • Multi Populations _ GUI
  • Multi Populations _ Pipeline
  • Random Simulation _ GUI
  • Random Simulation _ Pipeline
• Phenotype Simulation
  • Phenotype _ GUI
  • Phenotype _ Pipeline
• Population Structure
  • Population structure _ GUI
  • Population structure _ Pipeline
• Quality Control
  • Quality control _ GUI
  • Quality control _ Pipeline
• GWAS
  • GWAS _ GUI
  • GWAS _ Pipeline
• Method Evaluation
  • Method Evaluation _ GUI
  • Method Evaluation _ Pipeline
• FAQ and Hints

<!-- /TOC -->

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Installation

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Environment Setup

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JDK1.8 should be installed and environment variables must be configured before using G2P (http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)

Windows

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GUI
Download all files from https://github.com/XiaoleiLiuBio/G2P/tree/master/gG2P_win_64 and double click the .jar file
Pipeline
Download all files from https://github.com/XiaoleiLiuBio/G2P/tree/master/kG2P_win_64

Mac

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GUI
Download all files from https://github.com/XiaoleiLiuBio/G2P/tree/master/gG2P_mac and double click the .jar file
Pipeline
Download all files from https://github.com/XiaoleiLiuBio/G2P/tree/master/kG2P_mac
permission setting

$ chmod 777 gemma oldplink plink  

Linux

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GUI
Download all files from https://github.com/XiaoleiLiuBio/G2P/tree/master/gG2P_linux_x86_64 and run

$ Java -jar gG2P.jar  

Pipeline
Download all files from https://github.com/XiaoleiLiuBio/G2P/tree/master/kG2P_linux_x86_64
permission setting

$ chmod 777 gemma oldplink plink  

Data Preparation

All files should be prepared with the same prefix

ped

details see http://zzz.bwh.harvard.edu/plink/data.shtml#ped
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|Family ID|Individual ID|Father ID|Mother ID|Sex|Trait|marker 1|marker 2|marker 3|marker 4|marker 5|marker 6| | :---: | :---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: | |1|33-16| 0| 0| 0| 2| 0 0| A A| A A| A G| A G| A G| |1|38-11| 0| 0| 0| 2| 0 0| A G| A G| A A| A G| A G| |1|4226 | 0| 0| 0| 2| 0 0| A G| A A| A A| A G| A G| |1|4722| 0| 0| 0| 2| 0 0| A G| A G| A A| A G| A G| |1|A188 | 0| 0| 0| 2| 0 0| A A| A A| A A| A G| A G| |1|A214N| 0| 0| 0| 2| 0 0| A G| A A| A G| A A| A G| |1|A239 | 0| 0| 0| 2| 0 0| A A| A A| A G| A G| A A|

|Family ID|Individual ID|Father ID|Mother ID|Sex|Trait|marker 1|marker 2|marker 3|marker 4|marker 5|marker 6| | :---: | :---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: |:---: | |1|33-16| 0| 0| 0| 2| 0 0| 1 1| 1 1| 1 3| 1 3| 1 3| |1|38-11| 0| 0| 0| 2| 0 0| 1 3| 1 3| 1 1| 1 3| 1 3| |1|4226 | 0| 0| 0| 2| 0 0| 1 3| 1 1| 1 1| 1 3| 1 3| |1|4722| 0| 0| 0| 2| 0 0| 1 3| 1 3| 1 1| 1 3| 1 3| |1|A188 | 0| 0| 0| 2| 0 0| 1 1| 1 1| 1 1| 1 3| 1 3| |1|A214N| 0| 0| 0| 2| 0 0| 1 3| 1 1| 1 3| 1 1| 1 3| |1|A239 | 0| 0| 0| 2| 0 0| 1 1| 1 1| 1 3| 1 3| 1 1|

map

details see http://zzz.bwh.harvard.edu/plink/data.shtml#map
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|Chromosome ID|Marker ID|Genetic Distance|Physical Distance| | :---: | :---: |:---: |:---: | |1| PZB00859.1| 0| 157104| |1| PZA01271.1| 0| 1947984| |1| PZA03613.2| 0| 2914066| |1| PZA03613.1| 0| 2914171| |1| PZA03614.2| 0| 2915078| |1| PZA03614.1| 0| 2915242| |1| PZA00258.3| 0| 2973508|

pop

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new samples will be generated using samples within sub-population

|Sample ID|sub-Population ID| | :---: | :---: | |33-16| 1| |38_11| 1| |4226| 1| |4722| 2| |A188| 2| |A214N| 2| |A239| 2| |A272| 2| |A441-5| 2| |A554| 3| |A556| 3| |A6| 3| |A619| 3|

qtn

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each column represents simulated QTNs for each phenotype

|Phenotype 1|Phenotype 2|Phenotype 3|Phenotype 4|Phenotype 5| | :---: | :---: | :---: | :---: | :---: | |66 |67 |80 |83 |90| |9 |15 |52 |59 |135| |90 |96 |143 |147 |174| |3 |3 |15 |58 |89| |89 |118 |185 |203 |212| |69 |72 |72 |84 |110| |46 |59 |125 |204 |207| |14 |15 |19 |29 |39| |9 |23 |65 |111 |131| |19 |52 |74 |179 |194|

Genotype Simulation

Single Population _ GUI

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<p align="center"> <a href="https://raw.githubusercontent.com/XiaoleiLiuBio/G2P/master/results/Single Population.png"> <img src="results/Single Population.png" height="400px" width="460px"> </a> </p>

Ped: ped file
Map: map file
Path for output Ped/Map: path for output ped and map file
Block: Yes or No, if "Yes", the whole genome will be divided into blocks and shuffled to generate new samples
Number of SNPs in each block: Number of SNPs in each block
Mutation rate: the frequency of new mutations
Imputation: if TRUE, major allele will be used to impute missing values
Population size: simulated sample size

Single Population _ Pipeline

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Windows

java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.map --outgen D:\data\output --rn 100 --block 4 –impute
java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.map --outgen D:\data\output --rn 100 --block 4 --mutation 0.0001 --impute

Linux/Mac

java -jar kG2P.jar --ped /root/data/AG.ped --map /root/data/AG.map --outgen /root/data/output --rn 100 --block 4 –impute
java -jar kG2P.jar --ped /root/data/AG.ped --map /root/data/AG.map --outgen /root/data/output --rn 100 --mutation 0.0001
java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.map --outgen D:\data\output --rn 100 --block 4
java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.map --outgen D:\data\output --rn 100 --impute
java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.map --outgen D:\data\output --rn 100
java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.map --outgen D:\data\output --rn 100 --mutation 0.0001

jar: executive software
ped: ped file
map: map file
outgen: output path
block: number of SNPs in each block
rn: simulated sample size
impute: if 'impute' is added, major allele will be used to impute missing value
mutation: the frequency of new mutations

Multi Populations _ GUI

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<p align="center"> <a href="https://raw.githubusercontent.com/XiaoleiLiuBio/G2P/master/results/Multi Populations.png"> <img src="results/Multi Populations.png" height="400px" width="460px"> </a> </p>

Ped: ped file
Map: map file
Pop: pop file
Path for output Ped/Map: path for output ped and map file
Block: Yes, or No, if "Yes", the whole genome will be divided into blocks and shuffled to generate new samples
Number of SNPs in each block: Number of SNPs in each block
Mutation rate: the frequency of new mutations
Migration rate: the ratio of immigrants (or emigrants) for each group
Genetic drift: is the change in the frequency of an existing gene variant (allele) in a population due to random sampling of organisms
Imputation: if TRUE, major allele will be used to impute missing values
Sample size of each population: sample size of each newly simulated population 
Population size: number or vector, simulated sample size

Multi Populations _ Pipeline

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Windows

java -jar kG2P.jar --ped D:\data\AG.ped –map D:\data\AG.map --pop D:\data\AG.pop --outgen D:\data\output --block 4 --rn 100
java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.map --pop D:\data\AG.pop --outgen D:\data\output --block 4 --rn 100 --mutation 0.0001 --mig 0.1 --genetic 0.001

Linux/Mac

java -jar kG2P.jar --ped /root/data/AG.ped --map /root/data/AG.map --pop /root/data/AG.pop --outgen /root/data/output --impute --block 4 --rn 100
java -jar kG2P.jar --ped /root/data/AG.ped --map /root/data/AG.map --pop /root/data/AG.pop --outgen /root/data/output --rn 100 --mutation 0.0001 --mig 0.1 --genetic 0.001
java -jar kG2P.jar --ped /root/data/AG.ped --map /root/data/AG.map --pop /root/data/AG.pop --outgen /root/data/output --rn 100 --genetic 0.001
java -jar kG2P.jar --ped D:\data\AG.ped --map D:\data\AG.