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Old 05-03-2011, 08:37 AM   #1
leofixings
Junior Member
 
Location: UK

Join Date: May 2011
Posts: 1
Default Similarity programs for SNP files

Hi,

I'm a newbie to this field so please forgive the use of very basic language.

I've got two files. Each contains position and nucleotide information on each line.

Each file holds just the SNP information for a person. So for ex. for person A, the file would look like.
Chromosome 6: 133,088,927, G
Chromosome 6: 133,088,928, A
and so on.

The second file too has nucleotide information for the exact same locations.

Is there a utility somewhere that will show me the similarity between the two files? Something on the lines of BLAST which ofcourse requires the full sequence information and not just SNPs.

Prompt help will be much appreciated.

Thanks.

PS. the location information might not be exactly as detailed, I've oversimplified it for the sake of clarity.

Last edited by leofixings; 05-03-2011 at 08:38 AM. Reason: Missed out some information.
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Old 05-03-2011, 09:03 AM   #2
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700
Default comm

type "man comm" at command line and see if you can use the "comm" command. Perhaps simplly piping the output to "wc" might be a crude, but effective measure.

COMM(1) User Commands COMM(1)

NAME
comm - compare two sorted files line by line

SYNOPSIS
comm [OPTION]... FILE1 FILE2

DESCRIPTION
Compare sorted files FILE1 and FILE2 line by line.

With no options, produce three-column output. Column one contains lines unique to FILE1, column two contains
lines unique to FILE2, and column three contains lines common to both files.

-1 suppress lines unique to FILE1

-2 suppress lines unique to FILE2

-3 suppress lines that appear in both files
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