gravatar for curious

18 hours ago by

In the supplementary of phase 1 1000 genomes they say:

"The merged genotype likelihoods were used as the input to run the
BEAGLE software"

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?

link

modified 17 hours ago

written
18 hours ago
by

curious450



Source link