Run SNPtrio

Step 1 Please choose a SNP data file to upload. The current file size limitation is 250 MB per upload.
***Avoid starting filenames with numbers
(If you want to try a sample file, use sample SNP files from the links listed in our "Guide" section.)

Step 2 Please choose a trio definition file to upload:

(This file tells SNPtrio who is the child, the mother, and the father for each trio. The IDs in this file should be the the Call column headers used in your data file with the following removed: '.loh_Call' for Affymetrix CNAT 4.0; '.GType' for Illumina; '_Call' in other cases. SNPtrio uses the R Language, which only allows alphanumeric plus under line ('_') in variable names. R will replaced everything else with a '.' character. You do not need to modify the SNP data file. Just replace each space (' '), dash ('-'), etc. used in your SNP data file's column headers with a '.' character in this trio definition file. Tab is not allowed in the ID. R also requires variables to start with an alphabet. For IDs started with a numeric character, prefix them with an 'X' character in your trio definition file. If you want to try a sample file, use sample trio definition file from this site.)

Step 3 Data source:

(Affymetrix had changed CNAT's column headers in 4.0. If you use CNAT 4.0, open both '.cn.cnt' and '.loh.cnt' files for each sample. SNPtrio only uses these Affy columns: raw count, Probe Set, Chromosome, Physical Position, plua '.cn_Log2Ratio' and '.loh_Call' for each sample. You should hide all other columns, then, select 'Table export', in order to reduce your file size, thus resulted in shorter run time. SNPtrio uses '_Call' and '_SPA_CN' columns from earlier versions of CNAT.
Illumina user should keep only these columns in BeadStudio: Name, Chr, Position, plus '.GType' and 'Log R Ratio' for each sample. Hide all other columns prior to select 'Export Displayed Data to file..'.)

Affymetrix - CNAT 4.0

Affymetrix - ealier CNAT


Illumina - BeadStudio
Step 4 The height of plot in inches: 

Step 5 The width of plot in inches:

Step 6 The width ratio of label vs. plot:

Step 7 The scale of dots in SNPtrio plot: 

(Leave this scale at "0.1" for most cases. When a single chromosome is selected in Step 8 and your SNP source is from either Affymetrix or Illumina, you can use "0.4" to get a better view for overlapping dots.)

Step 8 Specify the minimum number of SNPs in an event region: 

(The number defines the minimum size of consecutive SNPs of the same class that your are interested in. A smaller number will resulted in more blocks to be found on the listing, and boxed on the plot. It should be an integer and larger than 1. The default is 3.)

Step 9 Specify chromosomes: 

(For most applications, leave this blank to select all chromosomes as a default. You can enter any chromosome numbers separated by spaces [e.g. 1 9 21], or a single chromosome group letter [A-G,X,Y]. Please use capital letters (e.g. X not x). Enter asterisk symbol '*' for all autosomes. Cytobands will be ploted when a single chromosome is entered here. Note: for HapMap data, you must select a single chromosome.)

Step 10 Do you want to include probability values on the plot?  

(Probability values are always available in the ".csv" file, but they can only be included in the plot when a single chromosome is selected.)


Step 11 For a single chromosome, do you want to include intensity ratio on the plot?  

(This option is available if you have selected a single chromosome. For Illumina, this is the "log R Ratio" column, i.e., the "Log2(Rsub/Rref)" plot on BeadStudio. For Affymetrix, this is the "Log2Ratio" column. HapMap currently does not have such information for downloading. Do NOT select "Yes" unless you have copy number data in your file.)


Step 12 Your data is based on which NCBI Build?

(Build 34 is also known as "July 2003", or "hg16" in UCSC Genome Browser. Build 35 is known as "May 2004", or "hg17", and Build 36 is known as "March 2006", or "hg18", respectively. Affy's CNAT 3.0 uses Build 35. Our sample data files use Build 35.)

Build 34

Build 35

Build 36

Build 37
Step 13 Enter an e-mail address here to receive your results. Leave it blank to receive your results in this browser.

(Due to the large number of SNPs in HapMap, you should enter an e-mail address here if you are running more than a couple of HapMap trios, to avoid your browser's time-out.)

Step 14 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 SNPtrio some time before your results are sent back to you. Please be patient!)