SNP Id Geno
1 a AB
2 a AB
3 a BB
. . .
. . .
. . .
1 b AB
2 b BB
3 b AB
. . .
. . .
. . .
1 c AA
2 c AB
3 c AA
. . .
. . .
. . .

SNP Genoa Genob Genoc . . .
1 AB AB AA
2 AB BB AB
3 BB AB AA
. . . .
. . . .
. . . .

sed 'G;s/^SNP.*/SNP/
/^1 /s/ ([^ ]*) .*SNP[^[:cntrl:]]*/& Geno1/
s/^([0-9]*) [^ ]*( [AB]*)n(.*n1 [AB ]*)/32/
s/^([0-9]*) [^ ]*( [AB]*)(n)(.*)/4312/
h
$!d' file1 > file2

awk '{if ($1==1) h=h" Geno"$2
if ($1!="SNP") g[$1]=g[$1]" "$3}
END {print "SNP"h; for (i in g) print i g[i]}' file1 > file2

awk '{g[$1] = g[$1] " " $3}
     END {for (i in g) print i g[i]}' < file1 > file2

awk '! ($1 in g) {snp[n++] = $1}
     {g[$1] = g[$1] " " $3}
     END {for (i = 0; i < n; i++) print snp[i] g[snp[i]]}' < file1 > file2

awk 'NR == 1 {header = $1; prefix = $3; next}
     first == "" {first = "" $1}
     $1 == first {header = header " " prefix $2}
     ! ($1 in g) {snp[n++] = $1}
     {g[$1] = g[$1] " " $3}
     END {
       print header
       for (i = 0; i < n; i++) print snp[i] g[snp[i]]
     }' < file1 > file2

perl -lane '
   next if $. == 1;                                     # skip header
   $A[@A] = $F[1] if /^1h/;                            # populate new header
   push @{$h{$F[0]}}, $F[2]}{$,="t";                   # OFS = tab
   print q/SNP/, map { "Geno$_" } @A;                   # new header print
   print $_, @{$h{$_}} for sort { $a <=> $b } keys %h;  # result
' gene.data

sed -e '
   1d; # monospace lines
   s/[[:blank:]]{1,}/t/g;s/^[[:blank:]]*//;s/[[:blank:]]*$//
   H;g
   #  1   2                            3                     4
   s/(n(.*n){0,1})1[[:blank:]]([^[:space:]]{1,})([[:blank:]][^[:space:]]{1,})$/tGeno31n14/
   /(n[^[:space:]]{1,}[[:blank:]])[^[:space:]]{1,}[[:blank:]]([^[:space:]]{1,})$/s//12/
   y/n_/_n/
   s/_([0-9]{1,})([^_]*)_(.*_){0,1}1([[:blank:]][^_]*)/_124_3/
   y/n_/_n/
   h;$!d
   s/n*$//
   s/n(n)/1/
   s/^[[:blank:]]/SNP&/
' gene.data

SNP     Genoa   Genob   Genoc
1       AB      AB      AA
2       AB      BB      AB
3       BB      AB      AA