2. Set the path on your system to use PLINK in any directory by
adding the following line in your “~/.bashrc” file using any
text editor.
export PATH="$PATH:/path/to/plink_directory"
3. You will have to restart your terminal to apply the changes.
3.1.3 Remove Short
Indels and Retain SNPs
Only
In this protocol we will only focus on SNPs. Thus, we will only keep
the data for the accessions obtained from the stock center and used
for GWAS.
$plink --vcf 1001genomes_snp-short-indel_only_ACGTN.vcf --recode --keep
glucose_sig_accessions.txt --out 1001genomes_snps_only_ACGTN
--vcf: input variant call format file
--recode: option set for PLINK to save the original allele labels.
We will retain the label for now.
--keep: input file containing the accession ids you would like to
keep. This is a tab-separated file with accession names on each line.
The file glucose_sig_accessions.txt can be downloaded from
https://netbiolab.org/wiki/glucose_sig_accessions.txt as a toy
example.
--out: output file prefix
The above operation results in four output files: 1001genomes_snps_only_ACGTN.log, 1001genomes_snps_only_ACGTN.
map, 1001genomes_snps_only_ACGTN.nosex, and 1001genomes_snps_only_ACGTN.ped.
3.1.4 Filter Out SNPs
That Have Minor Allele
Frequency of Lower Than
10%
The mixed model approach that we will use for association analysis
has the tendency to over-represent the significance of association
for alleles with less than 10% minor allele frequency [5]. This filterout step is required to prevent the over-representation.
$plink --file 1001genomes_snps_only_ACGTN --recode --maf 0.1 –out
1001genomes_snps_maf0.1_ACGTN
--file: input file prefix
--recode: option set for PLINK to save the original allele labels.
We will retain the label for now.
--maf: minor allele frequency threshold
--out: prefix of output files
The above operation results in four output files: 1001genomes_snps_maf0.1_ACGTN.log,
1001genomes_snps_maf0.1_ACGTN.map, 1001genomes_
snps_maf0.1_ACGTN.nosex, and 1001genomes_snps_maf0.1_
ACGTN.ped.
Genome-Wide Association Studies in Arabidopsis
191
adding the following line in your “~/.bashrc” file using any
text editor.
export PATH="$PATH:/path/to/plink_directory"
3. You will have to restart your terminal to apply the changes.
3.1.3 Remove Short
Indels and Retain SNPs
Only
In this protocol we will only focus on SNPs. Thus, we will only keep
the data for the accessions obtained from the stock center and used
for GWAS.
$plink --vcf 1001genomes_snp-short-indel_only_ACGTN.vcf --recode --keep
glucose_sig_accessions.txt --out 1001genomes_snps_only_ACGTN
--vcf: input variant call format file
--recode: option set for PLINK to save the original allele labels.
We will retain the label for now.
--keep: input file containing the accession ids you would like to
keep. This is a tab-separated file with accession names on each line.
The file glucose_sig_accessions.txt can be downloaded from
https://netbiolab.org/wiki/glucose_sig_accessions.txt as a toy
example.
--out: output file prefix
The above operation results in four output files: 1001genomes_snps_only_ACGTN.log, 1001genomes_snps_only_ACGTN.
map, 1001genomes_snps_only_ACGTN.nosex, and 1001genomes_snps_only_ACGTN.ped.
3.1.4 Filter Out SNPs
That Have Minor Allele
Frequency of Lower Than
10%
The mixed model approach that we will use for association analysis
has the tendency to over-represent the significance of association
for alleles with less than 10% minor allele frequency [5]. This filterout step is required to prevent the over-representation.
$plink --file 1001genomes_snps_only_ACGTN --recode --maf 0.1 –out
1001genomes_snps_maf0.1_ACGTN
--file: input file prefix
--recode: option set for PLINK to save the original allele labels.
We will retain the label for now.
--maf: minor allele frequency threshold
--out: prefix of output files
The above operation results in four output files: 1001genomes_snps_maf0.1_ACGTN.log,
1001genomes_snps_maf0.1_ACGTN.map, 1001genomes_
snps_maf0.1_ACGTN.nosex, and 1001genomes_snps_maf0.1_
ACGTN.ped.
Genome-Wide Association Studies in Arabidopsis
191