Filter Algorithms - Newport iServer MicroServer iTHX-M Operator's Manual

Filter Algorithms

380
Affymetrix GeneChip ®
• Sib pairs and parent-offspring pairs should have Mismatch scores
between 1.3-1.8
• Unrelated pairs should have Mismatch scores between .9 - 1.3.
The Mismatch chip variance can be used to resolve Sib and parent-
offspring relations.
The averaged Mismatch score is used for comparisons. The average is
calculated over all common SNPs.
AvgMismatchScore
where i is the SNP index. SNPs with nocalls are excluded from the
averaging.
N is the number of non-nocall SNPs
SNPS
For more information about generating a sample mismatch report, see
Using the Sample Mismatch Report Tool, on page
The export filter functions allow you to export only SNPs that meet
particular criteria:
• Allele Frequency (see page 381)
• Hardy-Weinberg Probability (see page 381)
• Mendelian Error (see page 382)
For more information about using the filter algorithms during SNP
exports, see Exporting Data in Tab-delimited Format, on page 230
Exporting Data for Association and Linkage Analysis Software, on
page 237.
Genotyping Analysis Software User's Guide
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NSNPS
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SNPS
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MismatchScore
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