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@pamu your solution requires that input file is sorted, the solution I posted didn't assume this, mostly because empyrean's posted code required sort:

cat file | awk '$3 ~/A|T|G|C/{print $0}'|...

I assume if second column is count of occurrences. then third row should contain 2 in second column.

This is lit bit nasty code..:D

awk 'function prnt() {
split(A[S],ARR);
...

Think this does what you want

awk '
$3!="." {
key=$1"\t"$2
if(!(key in I)) D[++keys]=key
if(!((key SUBSEP $3) in M)) {
I[key]++
K[key,I[key]]=$3
...

Hi pamu,
To answer your question about changing FS for different files: If you want to use the default setting for FS for the 1st input file and use another setting for FS for subsequent files, all...

perl -alne '{$h{"$F[1] $F[2]"}[0].=",$F[0]";$h{"$F[1] $F[2]"}[1].="$F[3];";}
END { foreach $item (sort keys %h ) {
$Tget="$h{$item}[0] $item $h{$item}[1]";$Tget=~s/(^,|;$)//g;print "$Tget"; }}'...

awk -f em.awk myFile
em.awk:

BEGIN {
c=","
sc=";"
}
{
idx=($2 OFS $3)
o[idx]=(idx in o)?o[idx] c $1:$1
f[idx]=(idx in f)?f[idx] sc $4:$4
}
END {
for (i in o)
print...

awk '{a[$2,$3]=a[$2,$3]?$1","a[$2,$3]";"$4:$0}END{for(i in a){print a[i]}}' file

Here is a way to do what I think you're trying to do using awk:
#!/bin/ksh
awk '
BEGIN { hdr2 = "Index" }
NF==1 { # WIth only one field, we have to be processing the index file.
if(FNR...

#! /bin/perl
open(IDX,"<Index") || die "Couldn't open index file";
@index=<IDX>;
close IDX;
$header{POSITION}="Position";
for($i=0;$i<$#ARGV+1;$i++)
{
$FH="F${i}";
open($FH,"< $ARGV[${i}]")...

Could you post the output of the following command:

od -bc file2 | head

How about this,
awk 'NR==FNR{a[$1]=a[$1]","$2;b[$1]=$3;next} b[$1] {print $0,a[$1],b[$1]}' file1 file2

I get this output:

zsh-4.3.11[t]% head file[12]
==> file1 <==
1 aa rep
1 dd rep
1 kk rep
2 bb sad
2 ss sad
3 ee dam

==> file2 <==
1 apple fruit
2 mango tree
3 lilly flower...