EMMAX Output to PLINK2: A Seamless Conversion Guide

Introduction to EMMAX and PLINK2

Genetic association studies have become increasingly popular in recent years, and with the advancement of technology, the amount of data generated has grown exponentially. Two popular tools used in these studies are EMMAX and PLINK2. EMMAX (Efficient Mixed-Model Association eXpedited) is a software package used for genome-wide association studies (GWAS) and genomic prediction, while PLINK2 is a comprehensive toolset for genetic association analysis. In this article, we will guide you through the process of converting EMMAX output to PLINK2 format, enabling you to seamlessly integrate the two tools in your workflow.

Understanding EMMAX Output

EMMAX output typically consists of a table with the following columns:

• CHR: Chromosome number
• SNP: SNP identifier
• BP: Base pair position
• A1: Allele 1
• A2: Allele 2
• FREQ1: Frequency of allele 1
• FREQ2: Frequency of allele 2
• P: P-value
• Beta: Beta coefficient

This output can be generated from various EMMAX commands, such as emmax-kin or emmax-kin-rg.

Converting EMMAX Output to PLINK2 Format

To convert EMMAX output to PLINK2 format, you will need to create a PED file and a MAP file. The PED file contains the genotype data, while the MAP file contains information about the SNPs.

Step 1: Create the PED file

Create a new file with the following format:

FAM_ID  IND_ID  PAT_ID  MAT_ID  SEX  PHENO  GENO1  GENO2 ...  GENOn

Where:

• FAM_ID is the family ID
• IND_ID is the individual ID
• PAT_ID is the paternal ID
• MAT_ID is the maternal ID
• SEX is the sex of the individual (1=male, 2=female)
• PHENO is the phenotype (0=unaffected, 1=affected)
• GENO1, GENO2,…, GENOn are the genotypes for each SNP

You can use the awk command to extract the genotype data from the EMMAX output:

awk '{print $1, $2, $3, $4, $5, $6, $7, $8}' emmax_output.txt > ped_file.txt

Step 2: Create the MAP file

Create a new file with the following format:

CHROM  ID  CM  POS  A1  A2

Where:

• CHROM is the chromosome number
• ID is the SNP identifier
• CM is the genetic distance (in centimorgans)
• POS is the base pair position
• A1 and A2 are the alleles

You can use the awk command to extract the SNP information from the EMMAX output:

awk '{print $1, $2, $3, $4, $5, $6}' emmax_output.txt > map_file.txt

Step 3: Convert the PED and MAP files to PLINK2 format

Use the plink2 command to convert the PED and MAP files to PLINK2 format:

plink2 --ped ped_file.txt --map map_file.txt --out plink2_output

This will generate a set of files with the .bim, .fam, and .bed extensions, which are the standard formats for PLINK2.

Notes

🔥 Note: Make sure to check the EMMAX output for any missing or incorrect data before converting it to PLINK2 format.

Conclusion

In this article, we have provided a step-by-step guide on how to convert EMMAX output to PLINK2 format. By following these steps, you can seamlessly integrate the two tools in your workflow and take advantage of the strengths of each tool. Remember to check the EMMAX output for any errors or inconsistencies before converting it to PLINK2 format.

What is EMMAX output?

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EMMAX output is a table with columns containing information about the SNPs, such as chromosome number, SNP identifier, base pair position, alleles, and p-values.

What is PLINK2 format?

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PLINK2 format consists of a set of files with the .bim, .fam, and .bed extensions, which contain information about the SNPs, individuals, and genotypes.

Why do I need to convert EMMAX output to PLINK2 format?

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Converting EMMAX output to PLINK2 format allows you to use the strengths of both tools in your workflow, such as taking advantage of PLINK2’s comprehensive toolset for genetic association analysis.