Two map/ped files refused to merge for some reason.
I followed this method here (Plink: Quick Way To Combine Two Datasets Using Only Common Markers by ff.cc.cc) to reduce the datasets to the same list of sites.
plink --bfile Deven --bmerge Harvard.fam Harvard.bim Harvard.bed --merge-mode 6 --out mismatchB
to identify the sites that had flipped genotypes, and I straightened them out using
plink --bfile Harvard --flip mismatchB.missnp --recode --make-bed --out HarvardFlipped
I converted them to map/ped from the binary format, and I tried to merge them and got an inexplicable map file error
ERROR: Problem with MAP file line: HGDP00001 HGDP00001 0 0 1 -9 G T A A C C G G A G G G A A C T G G A G T T T T G G C C C C A A T C C C C C G G G G T T T T G G A G T T C C A A A G C T A G C C G G A A G G C C T C C T A G A G G G G G A A T C T T T T G G G G A G G G C C T C G A G G G G C C T
I looked at the map and ped files and everything was fine. Any clue what is going on? I know that the Harvard dataset originally has coordinates using Hg18 and the Deven dataset has coordinates the using Hg19 (but the rs ids come from the same annotation file, which provided the conversion of Affy #s to dbSNP #s)