Hi All,
I recently converted a very large Topmed imputed VCF files into a plink format.
The command I used to convert this VCF was plink1.9 --vcf ${VCF} --make-bed --out ${VCF}_binary. Additionally, I also spent a significant amount of time performing QC on this plink file to remove problematic and poorly imputed variants.
This VCF has imputed dosages that I did not import while converting them to plink. I just realized that I should have imported the dosage information as well. I was reading the plink manual which says:
--vcf loads a (possibly gzipped) VCF file, extracting information which can be represented by the PLINK 1 binary format and ignoring everything else (after applying the load filters described below). For example, phase and dosage information are currently discarded. (This situation will improve in the future, but we do not have plans to try to handle everything in the file.)
Now that I have a filtered Plink file, I was wondering if I could import dosage information directly from the original VCF to my filtered plink. Could someone please share some insights? Thanks
You need to use plink 2.0 and its .pgen file format for this.