Helperfiles for using hmmix for calling archaic introgression into present day humans (both hg19 and hg38)

These files are:

1) Strict callability masks from 1000 genomes project in hg19 and hg38 coordinates

2) Outgroup files:

hg38_Outgroup_1000g_HGDP.txt: Frequencies of derived alleles in 490 present individuals with Sub-Saharan related ancestry: 426 from 1000genomes project and 64 from HGDP (total=490) Only first two columns are used by hmmix. The remaining columns what the reference base (hg38 refgenome), ancestral base, derived bases and the frequency of the derived bases in HGDP and 1000genomes

hg19_Outgroup_1000g.txt: Frequencies of derived alleles in 292 present individuals with Sub-Saharan related ancestry from 1000genomes

3) The mutation rate files are based on the outgroup files. They report the mutation rate in 1 Mb window scaled by the genomewide mutation rate 

4) The reference genome for hg19 and hg38

5) The ancestral allele calls for hg19 and hg38