I know there is a publish Endredo-Pecan-Ortheus five- or six-way genomic alignment, which has inferred the Human-Chimp common ancestor's alleles for sites across the genome. I have SNP data from the Affymetrix Human Origins arrays (both my own and previously published from the Reich lab) and overlapping common chimp/Neanderthal/Denisovan SNP data.

I am trying to calculate D statistics for the Neanderthal/Denisovan introgression, and it is common practice to use the Human-Chimp common ancestor's alleles in lieu of assuming the common chimp has the ancestral allele. I was wondering if anyone here has any experience on getting this type of data.

I know the Altai Neanderthal VCF files have it, and I could write a script to mine it out, but there must be a better way.

Thanks!