SNP  

Note: If you are using Excel to edit GenePattern files, be sure to save the file as a tab-delimited text file and supply the correct file extension. You can specify the file name in quotes to prevent Excel from appending .txt to the file name. Also, note that Excel's auto-formatting can introduce errors in gene names, as described in Zeeberg, et al (2004).

SNP File Format

This is a tab-delimited file format that contains SNP array data. The SNPFileCreator module can create non-allele-specific SNP files or allele-specific SNP files. A SNP file contains one row for each SNP and two or three columns for each SNP array. Non-allele-specific files contain two columns for each SNP array: the intensity value and the call. Allele-specific files contain three columns for each SNP array: the intensity value for allele A, the intensity value for allele B, and the call. Note: Not all SNP modules accept allele-specific SNP files.

The first line of a SNP file contains a list of labels identifying the SNP arrays.

Non-allele-specific

Example

Allele-specific

Example

The rest of the SNP file contains one row of data for each probe. Each row contains the probe intensity values and the SNP calls generated by the SNP microarray scanning software (such as Affymetrix's GeneChip software).

Non-allele-specific

Example

Allele-specific

Example

Sample SNP file: gistic_subset.snp, gistic_subset_allele_specific.snp

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