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KKI's SNP Analysis Tool is used to analyze Affymetrix (10K & 100K) SNP chip results from several perspectives. See options in Step 6 below.

The first line of the input file will be ignored, assuming it is a header line. The remaining lines of the input file are treated as data lines and contain the following eight tab-delimited columns, as shown below. Note that while some of the fields can be left blank, each data lines shall still contain seven tabs. KKISNP assumes the data lines had been sorted: first by Chromosome Number, followed by Chromosome Location.

    1.  SNP_ID
    2.  Chromosome Number without prefixes like "chr", "chrom"
    3.  Chromosomal Location USCS-GB track "Base Position"
    4.  Call AA, BB, AB, or NoCall
    5.  Copy Number USCS-GB track "CN"
    6.  Significance of the Copy Number       -/+log10(p-value)
    7.  Meta Analysis Significance -/+log10(meta p-value)
    8.  LOH UCSC-GB track "LOH"

The consecutive homozygosity (AAs and BBs) segments will be searched and reported. A single NoCall between AAs and/or BBs is included as part of a consecutive homozygosity region. The "score" in the GFF output is the value of either Copy Number or LOH value times 100. While the track labeled "CN" shows the Copy Number values for each SNP, the track labeled "CNR" shows the averaged Copy Number value for each consecutive region.
Step 1 Choose a file to upload:
Step 2 Enter a minimum value and a maximum value. This is used to limit the length the regions in SNP counts, in Mbp, or the value of LOH (depending on the option you choose in Step 6). minimum value:     maximum value: 
Step 3 Enter a track title (this step is optional):
Step 4 Enter a source name. This will be displayed as a track name on the UCSC Genome Browser.
Step 5 Choose a display type:
Consecutive NoCall Graph Table     by SNP counts
Consecutive Homo/Hemizygosity Graph Table     by SNP counts
Consecutive Homo/Hemizygosity Graph Table     by bp Size
Consecutive Homo/Hemizygosity Graph Table     by LOH values
SNP Copy Number Graph Table     by bins of 0.5 copy
Individual SNP LOH Graph

show only     or larger in Table  
Step 6 Enter a chromosome number or a chromosome group letter. (Leave this blank to select all chromosomes; enter an asterisk (*) for all autosomes)
Step 7 Click on the Submit button:
Depending on the size of your file, the work load of the server and the traffic load of the network, it may take SNPscan some time before your results are sent back to you. Please be patient!


To generate SNPscan Plots, go to the SNPscan page.
Return to the SNPscan home page.

Please send questions or comments to ting@kennedykrieger.org or pevsner@kennedykrieger.org.

Last updated: September 26, 2005.