The ASPEX package: affected sib-pair exclusion mapping

David Hinds and Neil Risch

1. Introduction

2. Compiling the programs under UNIX

3. Basic syntax and parameter specifications

4. Marker data format

5. The sib_ibd program

• 5.1 Command syntax
• 5.2 TCL parameters
• 5.3 Output

6. The sib_tdt program

• 6.1 Command syntax
• 6.2 TCL parameters
• 6.3 Output

7. The sib_phase program

• 7.1 Command syntax
• 7.2 TCL parameters
• 7.3 Output

8. The sib_map program

• 8.1 Command syntax
• 8.2 TCL parameters
• 8.3 Output

9. The sib_kin program

• 9.1 Command syntax
• 9.2 TCL parameters
• 9.3 Output

10. The sib_clean program

• 10.1 Command syntax
• 10.2 TCL parameters
• 10.3 Output

11. Other useful add-ons

• 11.1 The ligate filter
• 11.2 The restrict filter
• 11.3 The list_untyped filter
• 11.4 The list_incompat filter
• 11.5 The rec_dist filter
• 11.6 The xmgr_map script

12. Tips and Tricks

• 12.1 Data organization
• 12.2 More command file tricks
• 12.3 Shortcuts for simple analyses
• 12.4 The example subdirectory

13. Diagnostic messages