Table of contents

Practicalities: Tools for SNP discovery and association analysis Ross Lazarus MB,BS MPH From Genome to Disease NHLBI Symposium July 23/24 2003 Washington http://innatimmunity.net

Overview - Stages and methods

Web access to IIPGA tools

Advantages

Recommended preliminary analyses

Choose the “Prettybase Pipeline”

Set up report - title, data, outputs

Genotypes and exact HWE

2:Conservative, Low power

Same data, Pairwise r2

Slide 11

Same input, Ordered VG output

Images may be downloaded and saved

Outputs to spreadsheet or plain text

Genetic Context - SNPper Importer

SNP Biology - Annotated FASTA

Haplotype Inference

Use the prettybase to snphap tool

Slide 19

Raw SNPHAP output

Haplotype Tag SNP

Slide 22

Optimal sets of htSNP

5 htSNP for >5% Haplotypes?

Find the 3 sets of size 4

Use phase2best.

Slide 27

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Run SNPHAP -> htSNP

SNPHAP and htSNP

Use the ht SNP tester

Slide 32

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Haplo.glm

Haplo.GLM

Slide 38

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Author: Ross Lazarus, MB, BS MPH

E-mail: rerla@channing.harvard.edu

Homepage: http://innateimmunity.net/

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