Mapping 250K/500K SNP assay

chapter 7 | Analysis Workflow 201
SNPs and gender calls for each .chp file with every other .chp file in
the analysis group. The report shows every .chp file pair with
significant SNP overlap. It also shows pairs with the same sample IDs
but with significantly different genotyping calls.
The Sample Mismatch Report calculates the Mismatch metric for
every pair of .chp files. The Mismatch metric is the averaged IBS
(Identity by State), a measure of the number of alleles shared by two
individuals. This value increases with the degree of relatedness.
• Matched samples, replicates, or Identical twins should have
Mismatch values ~1.95 – 2.
• Sib pairs and parent-offspring should have Mismatch values ranging
from 1.3 - 1.8.
• Unrelated pairs should have Mismatch values between 0.9 – 1.3.
For more information about the calculation of the IBS metric, please
consult the GeneChip ® Genotyping Analysis Software User’s Guide.
To generate a Sample Mismatch Report:
1. Click the Mismatch Report button in the Genotyping Views
shortcut bar; or select Tools → Sample Mismatch Report from the
menu bar.
2. Drag and drop files from the Data Tree into the Mismatch Report
dialog box.
3. Set the Mismatch Threshold. Default is 1.95.
4. (optional) If you defined Sample identifiers as sample attributes,
you can uses these attributes to identify mismatch samples. Click
the Define Sample Attributes button to define the sample sample
attribute. You can also specify a gender attribute to detect gender
misregistrations.
The Sample Mismatch Report (Figure 7.9) is a tab-delimited text file
providing information on the experiment, input parameters, a legend
of the codes used in the Sample Mismatch Report, as well as a list of
data compared showing assigned and called gender, the Mismatch
score, and any problems detected in the pair-wise analysis.
For more information on the Sample Mismatch Report and Mismatch
score, please consult the GeneChip ® Genotyping Analysis Software User’s