How to convert the .vcf (imputed) file with GT:GP format to GT:DS?
You can do this in Hail.

Here's the rough code to do it (0.1 versions).

Setup:

from hail import *
hc = HailContext()


Import the .gen file. VCF works too:

dataset = hc.import_gen(
    'src/test/resources/example.gen', 
    'src/test/resources/example.sample')


Remap the genotype schema and export to VCF:

dataset.annotate_genotypes_expr('g = {GT: g.call(), DS: g.dosage()}')\
    .export_vcf('/tmp/out.vcf.bgz')


Take a look at the getting started page if you want to try it out!

I should note that you may be able to do QTL analyses in Hail, depending on the method you want to use. See blog post here.