Shell Programming and Scripting

ID    marker1        marker2         marker3      marker4    
b1    A         G        A         C         A          T      G         G     
b2    A         A        C         C         G          G      A         A

b1    marker1  A         G
b1    marker2  A         C
b1    marker3  A         T
b1    marker4  G         G
b2    marker1  A         A
b2    marker2  C         C
b2    marker3  G         G
b2    marker4  A         A

# awk 'NR==1{for(i=2;i<=NF;i++)a[i]=$i}
NR!=1{x=2;for(i=2;i<=NF;i+=2)print $1,a[x++],$i,$(i+1) }' file
b1 marker1 A G
b1 marker2 A C
b1 marker3 A T
b1 marker4 G G
b2 marker1 A A
b2 marker2 C C
b2 marker3 G G
b2 marker4 A A

perl -e '
open DATA, "<", "$ENV{HOME}/tmp/tmp.dat";  #Or wherever your data file is
$header=readline(DATA);                    # grab the headings
@header=split(/\s+/,$header);              # and parse them into separate fields
$waste=shift(@header);                     # Drop the pointless heading
while(<DATA>){                             # step through the rest of the file
	chomp;                                   # lose new lines
	@record=split(/\s+/,$_);                 # parse lines into fields
	for ($index=0;$index<@header;$index++){  # for each header field
	                                         # print out the 2 related entries in the format specified
		print "$record[0] $header[$index] $record[($index * 2 ) + 1] $record[($index * 2 )+2]\n";
	}
}'
b1 marker1 A G
b1 marker2 A C
b1 marker3 A T
b1 marker4 G G
b2 marker1 A A
b2 marker2 C C
b2 marker3 G G
b2 marker4 A A

awk '{for(i=2;i<=NF;i+=2)$i=(i==2?FS"":$1)FS"marker"i/2FS$i}1' infile | xargs -n 4