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The line numbers in 2 files are different (dont know which file is larger in terms of number of lines). so i was not able to compare them line by line which would have been a trivial task for me. i...

file1
chr pos1 pos2 pos3 pos4
1)chr1 1000 2000 3000 4000
2)chr1 1380 1480 6800 7800
3)chr1 6700 7700 1200 2200
4)chr2 8500 9500 5670 6670

file2
chr pos1 pos2 pos3 pos4...