Mapping 250K/500K SNP assay

chapter 7 | Analysis Workflow 191
3. Select the file set, project, sample, experiments, or analysis data in
the data tree and drag them to the Samples box.
4. (Optional) Choose any filters that need to be applied to the data.
The SNP filters allow you to filter out SNPs that do not meet the
particular requirements of your experiment from the export. You
can filter by:
• Allele Frequency
• Hardy-Weinberg Probability Value
• Mendelian error rate
When filtering on Mendelian error, you have the option to remove
the erroneous SNPs from the export files, or to set calls for
erroneous SNPs to NoCalls for families with inheritance errors.
You may want to use the second option if exporting multiple
families at once.
5. Select output file names and choose the path to save the files. Click
Export to export your data.
Consult the GeneChip ® Genotyping Analysis Software User’s Guide
for directions specific to each format type.
To batch export genotyping calls:
The Tab Delimited export tool allows batch export of genotyping calls
from large data sets simultaneously into tab delimited files. This
feature can be combined with File Sets to provide a flexible method of
analyzing custom groupings of large data sets.
The data is exported in a tab-delimited text file with the following
columns:
• Affymetrix SNP ID
• Genotype
1. Click the SNP Export button in the Genotyping Views shortcut
bar, or select Tools → Genotype → SNP Export… from the
menu bar.
2. Choose the Tab Delimited tab.