Format to convert...

gistfile1.txt

Example input...

# 
# More information on reference human assembly build 36:
# http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606&build=36
#
# rsid  chromosome      position        genotype
rs4477212       1       72017   AA
rs3094315       1       742429  AA
rs3131972       1       742584  GG
rs12124819      1       766409  GG
rs11240777      1       788822  GG
rs6681049       1       789870  CC


Example output

IndividualID rs123 rs456 rs456 …
N1234 A/C C/G T/T …
N1235 A/C G/G ?/? …
N3455 C/C G/G A/T …


Current solution:

perl -ane '$x{$F[0]}=$F[3]if$F[0]=~/^rs/&&$F[1]==6&&$F[3]=~/[ATCG]{2}/;END{print join(" ", "IndividualID", sort keys %x), "\n"; print join(" ", "NM3", for {substr($x{$_},1,0,"/");$x{$_}} sort keys %x), "\n"}' genome_Dan_Bolser_Full_20110223175600.txt > genome_Dan_Bolser_Full_20110223175600_chr6_unknown_format.txt