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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

SNP Chromosome PhysicalPosition array_1_name array_1_name Call array_N_name array_N_name array_N_name Call

Example

SNP Chromosome PhysicalPosition 100H_primary_GBM_101N 100H_primary_GBM_101N Call 100H_primary_GBM_56 100H_primary_GBM_56 Call

Allele-specific

SNP Chromosome PhysicalPosition array_1_name_Allele_A array_1_name_Allele_B array_1_name Call ...

Example

SNP Chromosome PhysicalPosition 100H_primary_GBM_101N_Allele_A 100H_primary_GBM_101N_Allele_B 100H_primary_GBM_101N Call ...

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

probe chromosome position array_1_intensity array_1_call array_N_intensity array_N_call

Example

SNP_A-1718890 1 2103664 1701.022 AB 1879.798 BB 947.904 BB

Allele-specific

probe chromosome position array_1_intensity_Allele_A array_1_intensity_Allele_B array_1 Call ...

Example

SNP_A-1718890 1 2103664 794.811 898.022 AB ...

Sample SNP file: gistic_subset.snp, gistic_subset_allele_specific.snp

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Updated on May 02, 2013 14:43