Exporting Data With The Snp Export Tool - Newport iServer MicroServer iTHX-M Operator's Manual

Exporting Data with the SNP Export Tool

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Affymetrix GeneChip ®
PerID 2
GCOSGen1
GCOSGen2
GTYPEeGen1
GTYPEGen2
NumberOfCalledSNP
NumberOfMatchSNP
IBSMetric
Has problem
You can use the SNP Export Tool to export SNP data in the following
formats:
• Tab-delimited format
• Haploview format
• GeneHunter open source software format
Genotyping Analysis Software User's Guide
Sample ID 2
Gender in the GCOS database for Chip 1.
Gender in the GCOS database for Chip 2.
Gender called by GTYPE for Chip 1.
Gender called by GTYPE for Chip2.
Number of SNPs used to calculate the IBS.
Number of called SNPS that matched between samples.
Mismatch score (also known as Identity by State, or IBS
metric) for the chip pair (for more information, see
Sample Mismatch Algorithm, on page
A code for the detection of problems:
0 = No problems
1a = Person IDs match but the Mismatch score (IBS
metric) is below the Mismatch threshold
1b = Persons genders match but the calculated genders
differ
2a = Person IDs differ but the Mismatch score (IBS
metric) is greater than the Mismatch threshold
2b = Persons genders differ but the Mismatch score (IBS
metric) is greater than the Mismatch threshold
2c = Persons genders match but differ from the
calculated genders
3 = The calculated genders differ but the Mismatch score
(IBS metric) is greater than the Mismatch
threshold
379).