Newport iServer MicroServer iTHX-M Operator's Manual page 236

TYPES OF SNP OUTPUT FILES
228
Affymetrix GeneChip ®
The SNP call data and pedigree data, if available, is exported in a set
of files. You can select from the following types of SNP data files:
• Tab-Delimited Output File Format (see below)
• Haploview File Formats, on page 228
• Merlin Output Files, on page 228
• GeneHunter Open Source Software Output Files, on page 229
linkage analysis)
Tab-Delimited Output File Format
The data is exported in a tab-delimited text file with the following
columns:
SNP ID Unique identifier for the SNP.
Chromosome Chromosome number for the SNP.
Position Chromosome position for the SNP
Genotype The SNP genotype call for the sample
Allele Frequency Minor allele frequency calculated for the SNP and samples.
Haploview File Formats
Haploview Export uses the same file format as Merlin (see below for
more information).
The marker file uses a tab-delimited file format with two columns,
with a line for each SNP. The first column contains the SNP name,
and the second column contains the chromosome position of the SNP.
Merlin Output Files
The Merlin file formats are described at http://www.sph.umich.edu/
csg/abecasis/Merlin/tour/input_files.html. The following table
summarizes the three types of files written:
Genotyping Analysis Software User's Guide
(for association analysis)
(for linkage analysis)
(for