KKI-SNP

KKI's SNP Analysis Tool is used to convert Affymetrix (10K & 100K) SNP chip results into the wiggle (WIG) format used by the UCSC Human Genome Browser to display patient SNP data as custom tracks. Click here to see a screen capture of a typical output (showing a deletion on chromosome 7p).

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"

Step 1	Choose a file to upload: (To try a sample data file that you can upload for Step 1, click here or visit the sample data page. Once you have created a WIG file on your hard drive, proceed to Step 10 below; if you want to see a WIG file and use it directly in Step 10, click here, and save as a text file. This case has a dramatic deletion on chromosome 7p.)
Step 2	Enter the file name of your selection here: (For example, for file C:\Documents and Settings\user\Desktop\data.txt, enter data.txt. This step is required, and it allows SNPscan to work with a variety of different browsers and operating systems.)
Step 3	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 (most users should use the default values).	minimum value: maximum value:
Step 4	Enter a track title:
Step 5	Enter a source name. This will be displayed as a track name on the UCSC Genome Browser.
Step 6	Choose a label for the WIG format*. When you zoom in to the Genome Browser, you can visualize SNP IDs (these are linked to the NCBI Homo sapiens* map viewer), or p values, or meta p values.**
Step 7	Enter a chromosome number or a chromosome group letter. (Leave this blank to select all chromosomes; enter an asterisk (*) for all autosomes.)
Step 8	Click on the Submit button (and be sure to read steps 9 and 10 as well): 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!
Step 9	Your WIG file will appear after you click Submit. "Save as" a text file to your hard drive. The central black line on the Copy Number track is defaulted to 2.47, based on SNP data generated by groups with limited experiences working on Affymetrix SNP chips. SNP data downloaded from Affymetrix typically has a mean copy number around 2.1 for autosomes. To adjust this default value, edit the text file you saved at Step 9 and globally replace "yLineMark=2.47" with your desired value.
Step 10	Go the the UCSC Human Genome Browser (http://genome.ucsc.edu/cgi-bin/hgGateway). Make sure that to choose the appropriate assembly date at the UCSC site. If you use Affymetrix CNAT v.3.0, use the May 2004 (Build 35) UCSC version. If you use earlier Affymetrix CNAT versions, without updating your annotation file, you are most likely to need the "July 2003" version (Build 34) to match the available SNP data. Select "add your own custom tracks" then upload your text file. Please be patient; in a few minutes, your SNP data will be visualized as a custom track!