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Seems to be working on your test files OK (see transcript below).

Perhaps your actual data dosn't match the posted testfiles?

$ cat file1
chrom 1 100 A G 20 ...(10...

How about these:

1)awk -F'\t' 'FNR==NR {
Rng[$1]=$2","$3
for(i=4;i<NF;i+=2) Rng[$1]=Rng[$1]","$i","$(i+1)
next }
($1 in Rng){
c=split(Rng[$1],v,",");
for(i=1;i<c;i++)
if($2...