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,
