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Friday, November 22, 2013

Find SNP Overlap from Different SNP Arrays

If you have .bed files for array manifests it is relatively easy to use UNIX to compare the overlap between SNP positions in the two files.  Here is a quick one line of code to do so:

This essentially finds all rows that are the same in the two files.  It requires all unique rows in each file and will only work for one base pair long items.

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