I was wondering if there are Plink files (or vcf which can be converted in Plink format) available for 1000Genomes where the alleles are coded as D (deletion) and I (insertion), rather than ACGT, and the names of the INDELs would be chr:pos:I or chr:pos:D instead of chr:pos:alleles.
One way could be to extract INDELs from the vcf 1000 Genomes, change these to I/D for alleles and chr:pos:I or chr:pos:D for names, and then use
--update-name and --update-alleles
If however there is a vcf file already in this format an easier way could be to make this vcf into Plink format using Plink2. Does anybody know whether this format exists?
Any feedback/suggestions if there is an easier way to do this is very much appreciated.