1 getting started download and install haploview

1

Getting Started

• Download and install Haploview http://www.broad.mit.edu/mpg/haploview/index.php

2

i. Downloading dense genotype/resequencing data from HapMap and SeattleSNPs

ii. Choosing tagSNPs by using Haploview

Lab 1

Yu-Chun Jean Yenyyen@hsph.harvard.eduBldg.2 Rm. 200

3

• HapMap: http://www.hapmap.org/

• Seattle SNPs: http://pga.mbt.washington.edu/

• “Prettybase Purifier” tool: http://innateimmunity.net/IIPGA2/index_html (register required)

• Haploview: http://www.broad.mit.edu/mpg/haploview/index.php

4

Click Here

5

Search IGF1

6

7

Zoom In

8

9

Using HapMap.Org : A Tutorial http://www.hapmap.org/downloads/presentations/hapmap.org.ppt

ASHG 2007 HapMap Tutorial http://www.hapmap.org/downloads/presentations/ASHG07_HapMapTutorial.ppt

10

Select “Download SNP genotype data”

Click Here

11

Click Here

Choose

12

Click Here

13

Click Here

14

Right click to save

15

079773 E008 G G079773 E009 G G079773 E010 C C079773 E011 G G079773 E012 G G079773 E013 C C079773 E014 C G079773 E015 G G079773 E016 G G079773 E017 C G079773 E018 C G079773 E019 C G079773 E020 G G079773 E021 G G079773 E022 C C079773 E023 N N080761 D001 aa aa080761 D002 aa -080761 D003 aa aa080761 D004 aa aa080761 D005 aa aa080761 D006 aa aa080761 D007 aa aa080761 D008 aa aa080761 D009 aa aa080761 D010 aa -080761 D011 aa aa080761 D012 aa aa080761 D013 aa aa

“Prettybase” format

SNP (relative pos)

SubjectAlleles

Contains insertion-deletion polymorphisms (INDELS)

This can be a problem for many software tools, which expect SNPs – also indels present genotyping difficulties

Can clean file using “prettybase purifier” tool at

http://innateimmunity.net/IIPGA2/index_html (register required)

16

Click Here

17

Click Here

18

Can restrict subjects to a given ethnicity

Can restrict SNPs to those with MAF above a user-defined threshold

Can eliminate INDELS

19

079773 E008 G G079773 E009 G G079773 E010 C C079773 E011 G G079773 E012 G G079773 E013 C C079773 E014 C G079773 E015 G G079773 E016 G G079773 E017 C G079773 E018 C G079773 E019 C G079773 E020 G G079773 E021 G G079773 E022 C C079773 E023 N N080761 D001 aa aa080761 D002 aa -080761 D003 aa aa080761 D004 aa aa080761 D005 aa aa080761 D006 aa aa080761 D007 aa aa080761 D008 aa aa080761 D009 aa aa080761 D010 aa -080761 D011 aa aa080761 D012 aa aa080761 D013 aa aa

“Prettybase” format

SNP (relative pos)

SubjectAlleles

Contains insertion-deletion polymorphisms

This can be a problem for many software tools, which expect SNPs – also indels present genotyping difficulties

Can clean file using “purifier” tool at http://innateimmunity.net/IIPGA2/index_html.

Many software tools don’t like this formatHaploview, for example, wants “pedigree” file (short and fat instead of long and skinny) and “info” file (with SNP positions).

Can convert using makehv (R function) or %haploview (SAS Macro), available at http://www.hsph.harvard.edu/faculty/kraft/soft.htm.

[caveat emptor: this code is unsupported!]

20

ped.id subject.id dad.id mom.id gender affection.status snp1.allele1 snp1.allele2 etc.

21

22

Click Here

23

24

Click Here

25

26

27

Click Here

28

Force Include: have to genotype this SNP

[e.g. nsSNP]

Force Exclude: cannot genotype this SNP

[e.g. known not to genotype well in your lab]

Can combine “force include” and “force exclude” to

evaluate how well a given set of SNPs performs

Can decide what r2 performance you are willing to live with, whether you want to

pursue “aggressive” tags

Click Here

29

SNPs you should genotype, tests

you should perform

How many SNPs does the

highlighted marker “tag”

30

Law of diminishing returns: you have

to do a lot of genotyping to

capture last few stragglers

31

32

ped file

info file

33

Getting ready for next Lab session

• Request IT Help Desk for a Unix Account.IT Helpdesk (LL-15) from 8:00 – 5:00pm, at 617-432-HELP, or helpdesk@hsph.harvard.edu.

• Unix computing guide for beginners: http://www.isites.harvard.edu/icb/icb.do?keyword=k2067&pageid=icb.page23341