Shell Programming and Scripting

I have a tab-delimited file containing a large genetic dataset with binary base calls, in this format:

Code:

Chr7 26021407 1/1:0,0,0:5 1/1:0,0,0:5 1/1:0,0,0:5
Chr7 26022023 1/1:0,0,0:3 1/1:0,0,0:3 1/1:28,3,0:5
Chr7 26022087 1/1:0,0,0:6 1/1:25,3,0:9 1/1:25,3,0:9
Chr7 26022656 1/1:0,0,0:3 1/1:27,3,0:5 1/1:0,0,0:3
Chr7 26022752 1/1:21,3,0:5 0/1:0,0,0:3 1/1:24,3,0:5
Chr7 26022759 0/1:15,3,0:4 0/1:0,0,0:3 0/1:18,3,0:4
Chr7 26022873 1/1:36,3,0:7 1/1:0,0,0:4 1/1:16,3,0:7
Chr7 26022940 1/1:0,0,0:5 1/1:28,3,0:8 1/1:14,3,0:8
Chr7 26023652 1/1:0,0,0:6 1/1:0,0,0:6 1/1:25,3,0:8

The 2 leading columns are coordinate information, then there are some columns with other information (omitted from this example), and the SNP data (the data of interest, columns beginning 0/0, 0/1, or 1/1) begin at column 10. The number of subsequent columns matches the number of samples.

I would like to identify and eliminate any line in which all of the SNP call data (the leading 0/0,0/1, or 1/1) match across the dataset, and are therefore uninformative in my analyses. What I have in mind would function like this:

Code:

awk '{if (substr($10,1,3)==substr($11,1,3) && substr($10,1,3)==substr($12,1,3).... [include all columns from $10 to end]) {next}} {print}' [infile]

But I want to be able to specify a range of substrings to compare across, rather than entering each one manually, which seems tedious and unnecessary. Any help with this would be hugely appreciated.

thanks a lot!

try:

Code:

awk -v sc=10 '{c=0; for (i=sc+1; i<=NF; i++) if (substr($i,1,3)!=substr($sc,1,3)) c++; if (c) print}' infile