VCF TO PED FORMAT USING PLINK 2 - HOW TO RUN GWAS

[Helena]

Hi everyone,

I am very new to PLINK and I kind of got lost between the commands in each PLINK version. I have vcf files which I need to turn into .ped and .map so I am able to see my samples and then move on to perform GWAS.

I am now using plink2 and I typed the following command at first:

../plink2 --double-id --vcf /groupvol/med-bio/epiUKB/projects/genomics_of_lipidomics/hase_affy/raw/chr21/chr21.dose.vcf.gz --chr 21 --from-bp 9411245 --to-bp 9411245 --recode --out results

which kept giving me the error: Error: Only VCF, oxford, bgen-1.1, haps, hapslegend, A, AD, A-transpose, and ind-major-bed output have been implemented so far.

After a lot of attempts, I used:

../plink2 --double-id --vcf /groupvol/med-bio/epiUKB/projects/genomics_of_lipidomics/hase_affy/raw/chr21/chr21.dose.vcf.gz --chr 21 --from-bp 9411245 --to-bp 9411245 --recode vcf --out results

which gave me an output but it was still vcf because I didn't know which other option to choose.

If someone can help me, that would be of such an amazing help and relief!

Thanks a lot!

[Christopher Chang]

If you need to do anything with .ped/.map files, use PLINK 1.9.  PLINK 2.0 is currently in alpha testing, and several functions (including .ped/.map import and export) are being deliberately left out until the end of the alpha test.