clarify documentation of the phenotype.updateparents.txt file
update README with clarification about pheno.updateparents.txt
begin adding support for CytoChip
get high heterozygosity variants and find ones spaced at least 0.7 cM apart to generate linkage grid

need to add POD documentation at the bottom
fixed syntax mistake in edit_linkage_family_info.pl
reordered process so that the $pheno.flipped binary PLINK files contain all variants with alleles flipped to match the reference .freq files

Now produces $outdir/*.plink.frq file with plink --read-freq --genome to get IBD for use in PRIMUS and other applications
Merge branch 'makefileswithallvar' into develop
Support cytochip
updated documentation