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With a question like this, it is ALWAYS a good idea to tell us what operating system and shell you're unison. With a POSIX conforming shell, you could try something like:
#!/bin/ksh
last=""
while...

A hint:

while read VAR1 VAR2
do
echo $VAR2 " " $VAR1
done<your_file

With the above you should be able to figure out the next step...

Cheers

Do those input files share the column 1 values? If so, did you consider the join command?

Try:echo "Enter INPUT:"
read INPUT
echo "Enter OUTPUT:"
read OUTPUT
cut -f1-4 $INPUT | sed 's/hello/goodbye/g' | sort -uV > $OUTPUT

looks like the below line from the expect output is incorrect
chr1 153234602 155205669 GBA 1971067
it should be
chr1 155205331 155205669 GBA 338
If my assumption is true, below code...

You could first print an empty line when column 4 is not "hom". Then pipe that output to another awk which uses empty lines as a record separator then the start is in $2 (field 2) and the last is in...

awk '{s[$2]=$0; c[$2]++} END {for (i in s) print s[i],c[i]}' *.tabBy indexing with field $2, a duplicate is overwritten in array s, and further increases the count in array c. Array s simply stores...

A quick hack is to directly print the 1st line of each file, and proceed with the next cycle.
awk 'FNR==1 {print; next} ...
You need GNU awk or nawk or Posix awk for that.