In the supplementary of phase 1 1000 genomes they say:
"The merged genotype likelihoods were used as the input to run the
In the more recent recalling of 1000G on GRCh38 they mention a similar approach
The VCF file containing the genotype likelihoods ...were processed in
parallel by Beagle 14 by using the following command:
java -jar beagle.08Jun17.d8b.jar chrom=$chr:$start-$end gl=$chr.biallelic.GL.vcf.gz out=$chr.$start.$end.beagle niterations=15
Little baffled because usually I think of genotype imputation using a reference panel. Are the haplotypes where where enough coverage existed being used to determine variation in those haplotyes where not enough coverage existing to call by observation?