Okay I'll start over and try to be more exact.
I am looking at a file that has about 3 million rows and about 100 columns. The row number is given by the index number, in the 1st column, as previously shown. The genotypes that I need to look at, 'TT' or 'GG', for example, are located in the 88th column. The last column of importance is the 6th in which it gives the name of the mutation, such as 'intronic'.
In a seperate file, there are two columns. The first being the index number that ranges from 1 to about 3 million, and the second has static values for the references, i.e 'T' or 'G'.
I would like to compare the letters in index 1 of the first file with index 1 of the second file, and so on and so forth.
Now I am changing one aspect of this so I apologize.
If either one of the letters from the first file at index 1 matches the letter from the second file at index 1, I would like for the 1st column and 6th column of the first file to be printed out.


For example:

Code:

 
File #1
Column 1     ....        Column 6     .....   Column 88
(Index)                   (mutation)            (Genotype)
1                             Intronic                 TT
2                             Frameshift             GT
3                             Exonic                   AT
4                             Exonic                   AA
5                             Intronic                 GC
 
File #2
Column 1      Column 2
(index)          (reference letter)
1                      A
2                      C
3                      C
4                      A
5                      G

Output: Since at index 4 and 5, one of the letters in the genotype in file 1 match the letter from file 2, i would like the following to be displayed:

Code:

 
4 Exonic 
5 Intronic

I hope this is more helpful