short description on how to use dchip snp
DESCRIPTION
Short description on how to use dChip SNP. Please watch in slide show mode Updated 02-24-2004. dChip SNP. Available upon request from Cheng Li Please send Email to: Cheng Li at: [email protected] Parametric linkage analysis Dominant Recessive - PowerPoint PPT PresentationTRANSCRIPT
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Short description on how to Short description on how to
use dChip SNPuse dChip SNP
Please watch in slide show modePlease watch in slide show mode
Updated 02-24-2004Updated 02-24-2004
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dChip SNPdChip SNP
• Available upon request from Cheng LiAvailable upon request from Cheng Li• Please send Email to:Please send Email to:
– Cheng Li at: Cheng Li at: [email protected]@hsph.harvard.edu
• Parametric linkage analysisParametric linkage analysis– DominantDominant– RecessiveRecessive
• Genome annotation with Genes, Genome annotation with Genes, Cytoband, Lod score and SNP information Cytoband, Lod score and SNP information in one windowin one window
• No error correction needeNo error correction neede• Runs up to 17 bitesRuns up to 17 bites
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Step-by-StepStep-by-Step
• Export GDAS files Export GDAS files – Only the Affy SNPID and Genotypes need to Only the Affy SNPID and Genotypes need to
be includedbe included
– Generate the standard pedigree file as Generate the standard pedigree file as discusseddiscussed
– Add an array column in the pedigree file Add an array column in the pedigree file before the affection statusbefore the affection status
– This column needs to have the identical name This column needs to have the identical name as the experiment name in GDASas the experiment name in GDAS
– For individuals without genotypes add “Nofile” For individuals without genotypes add “Nofile” in the fieldin the field
– Save as text file (tab delimited)Save as text file (tab delimited)
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dChip SNP : dChip SNP : Data fileData file
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dChip SNP : dChip SNP : Pedigree filePedigree file
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dChip SNP: dChip SNP: Import dataImport data
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dChip SNP: dChip SNP: Import dataImport data
1. Assign a name for the analysis
2. Select the data file
3. Select SNP analysis
4. PressOK
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dChip SNP: dChip SNP: Import dataImport data
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dChip SNP: dChip SNP: Import annotation filesImport annotation files (all files are distributed with the software)(all files are distributed with the software)
1. Select
2. Select
3. Select
4. Select(optional)
5. Select
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GenotypeInformation
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dChip SNP: dChip SNP: Linkage analysisLinkage analysis
Select the pedigree file
Define:Disease allele freq.PenetranceDisease model
Simulation?
Press: OK
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LOD Graph