September 18, 2012

This directory contains genotypes from Genome STRiP for sites from the Phase 1 integrated call set (autosome only)
genotyped on the Phase 2 AFR panel (191 samples).  The Phase 1 sites filters were applied post-genotyping,
which removed 425 sites (3%), as these sites did not genotype well in the smaller Phase 2 panel.

The VCF file contains two tags with genotype likelihoods:
GL: These are genotype likelihoods that employ a population-frequency prior in the read-depth genotyping.
GL0: These are genotype likelihoods that do not employ the population-frequency prior and are thus suitable for doing genotype refinement with beagle/MaCH.
The GT and GQ fields are based on the GL likelihoods.
Only sites that pass the post-genotyping site filters are included in this vcf file.

For questions contact Bob Handsaker ( handsake at broad institute dot org )