home | about | Oxford University | research | groups | public | links & resources | news | seminars | vacancies | contact | find us

SNP Selection Page

Input File Format

• Haplotypes are defined in a text-file with three columns separated by spaces.
• Each line defined one haplotype.
• Column 1 contains the name of the haplotype
• Column 2 contains the haplotype represented as a string of non-space characters. THERE MUST BE NO SPACES IN THE HAPLOTYPE. Each character represents an allele; the character at position n in the string represents the allele at marker n in the haplotype. Conventionally we represent diallelic markers such as SNPs by 1's and 2's. Since there are at least 62 alphanumeric characters, it is possible to represent highly polymorphic markers such as microsatellites, as well as simple diallelic markers such as SNPs.
• Currently missing values are not explicitly supported; however they can be coded simply as a distinct allele (for example '0'). Alternatively they can be coded as the most common allele. Note that the method of coding for missing values will affect the output; there appears to be no simple neutral way of dealing with missing data.
• Column 3 contains the population frequency of the haplotype, which can be 0
• Blank lines and lines containing Comments preceeded by # are ignored.

An example of the input format is given here:

	      
        
        #No	Haplotype               Frequency
        1	11112121121111222	0.01    
        2	11112121122112112	0.01	
        3	11121122212112112	0.01    
        4	11121122212122211	0.04    
        5	11211111121111222	0.01    
        6	11211112212112112	0.01    
        7	11211122212122211	0.01	
        8	11212111121111212	0.02    
        9	11212121111111222	0.01    
        10	11212121112112112	0.02    
        11	11212121121111112	0.01    
        12	11212121121111212	0.01    
        13	11212121121111222	0.04    
        14	11212121121112111	0.01	
        15	11212121121112112	0.03    
        16	11212121122111222	0.00	
        17	11212121122112112	0.10	
        18	11212221121112112	0.01	
        19	11221112212112212	0.01	
        20	11221112212122211	0.01	
        21	11221122212112212	0.03	
        22	11221122212122211	0.01	
        23	11221122212122212	0.02	
        24	11221221122212212	0.01	
        25	12111121122112112	0.01	
        26	12111122212122211	0.01	
        27	12121112212222211	0.02	
        28	12121121121111212	0.01	
        29	12121121121112112	0.01	
        30	12121121121112222	0.03	
        31	12121121122112112	0.08	
        32	12121121122122112	0.01    	
        33	12121122212112112	0.00		
        34	12121122212112112	0.11		
        35	12121122212112222	0.00		
        36	12121122212212112	0.05		
        37	12221122212212112	0.01		
        38	21121121122112112	0.05		
        39	21121122212112112	0.04		
        40	21121122212122211	0.02		
        41	21121122212212112	0.02		
        42	21221121122112112	0.01		
        43	21221121122112212	0.02		
        44	21221122212122211	0.02		
        45	22121122212111212	0.01		
        46	22121122212122211	0.04		
        47	22221211121111212	0.05		
        48	22221211121112112	0.01
        

Drop me an email for more details.