Explanation of how to use Illumina, Affymetrix, and HapMap data; sample data files; examples of typical outputs

You need to upload two files: a SNP data file which contains SNP genotype calls, and a trio definition file which identifies each trio. You can also include copy number (intensity) data to help interpret the SNPtrio output (e.g. to distinguish between uniparental disomy and a hemizygous deletion).

SNPtrio expects these three columns in the SNP data file: SNP ID, Chromosome, Physical Position, and followed by one column for each individual's genotype calls. SNPtrio supports SNP data from Affymetrix, HapMap, and Illumina. Click on these names to get a sample SNP data file in the format in which they were exported, prior to any modification.

How to use SNPtrio to analyze Affymetrix SNP data

Affymetrix : All you need to do is to export a tab-deliminated text files exported from Affymetrix's Copy Number Analysis Tool (CNAT) v2.0 or later, with the first line deleted (i.e., "Copy Number Analysis Tool" from CNAT 2.0/2.1 or "Copy Number Viewer" from GTYPE's CNAT Viewer). If you use CNAT 3.0 or GTYPE 4.0, do not use any file saved in the ".cnt" file format as your input for SNPtrio. Instead, select "Export", "Table" from GTYPE's CNAT Viewer menu bar to save your SNP data as a tab-delimited file. The first line of your input file should have column headers, as shown in this sample Affymetrix SNP file. For an Affymetrix data file, SNPtrio takes columns labeled as "XXXX_Call" as the SNP call columns. You should use the "XXXX" (ie., without the "_Call" portion) in your trio definition file. Additional columns are simply ignored. Click on here to get a sample definition file for this Affymetrix example. You should get this SNPtrio plot for this sample Affymetrix trio. Note that the child of this trio is a female with a mosaic chromosome X. You can get a copy of our SNPscan paper to get explanations on chromosome X of this female.
Click here for sample Affymetrix SNP data: sample Affymetrix SNP file and sample definition file
Click here for a screen capture of the SNPtrio output data for these files

How to use SNPtrio to analyze HapMap SNP data

HapMap : You can run downloaded HapMap SNP files without any modification. Due to HapMap's huge number of SNPs (281,000+ for chr1, 298,000+ for chr2, ..., 52,000+ for chr22), typical users should try to upload only one chromosome at a time, to keep your run time within your brower's time-out trigger. All you need to do is download HapMap's SNP data and provide a trio definition file. SNPtrio will ignore non-bi-allele or non-single-neucleotide SNPs ( Click here for sample HapMap SNP data: a HapMap SNP file , and a sample definition file)
Click here for a screen capture of the SNPtrio output data for these files

How to use SNPtrio to analyze Illumina SNP data

SNPtrio can handle Illumina SNP data. Use these steps in Illumina's BeadStudio to generate this format: select the "Full Data Table" tab; click on the "Column Chooser" icon; in the "Displayed Columns" area, keep "Name", "Chr" and "Position", hide the rest; in the "Displayed Subcolumns" area, keep "GType" and "Log R Ratio", hide the rest; click on "Export Displayed Data to File" icon; finally, save the file.
Click here for sample Illumina SNP data: sample Illumina SNP file (three 550K SNP arrays, 35MB) and this sample definition file
Click here for a screen capture of the SNPtrio output data for these files
The current file size limitation is 250 MB per upload.