Dear PLINK Community,

I hope this message finds you well. I have encountered a challenge while attempting to convert a VCF file into a format suitable for association analyses using BOLT-LMM. Despite several days of effort, I have been unable to find a solution.

I aim to convert my VCF file into a format representing imputed SNPs in a 2-dosage design, as suggested on the BOLT-LMM documentation page, using the command plink2 --dosage format=2.

https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html Section: 5.1.2

So far, I have used the following command to create a PLINK binary dataset:

plink2 --vcf mergedTemp.vcf dosage=DS --make-bed --out mitoDosage

However, my next step is to produce a file in the --dosage format=2 format, where I've hit a stumbling block.

Could anyone please guide me on generating a file in this specific format? I have attempted several alternatives, but none have yielded the desired results.

Any help would be greatly appreciated.

Best regards,