SNP High-Throughput Linkage Analysis System

Overview	FlowChart	License information	Download	System requirements	Version history
Installation	Supported programs	References	Links	Contact information

Overview

SNP HiTLink is a computer program providing a useful pipeline to directly connect SNP (Single Nucleotide Polymorphism) data and linkage analysis program.
SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro.
To run SNP HiTLink, two programs, SNP HiTLink (SNP HiTLink Ver.1.5.1) and run_linkage.pl (2010/05/10-r48 version), will be required. Use of previous versions of either program may result in incompatibilities.

SNP HiTLink consists of two processes. The former process creates necessary data files by the program described in the Visual Basic programming on Windows OS, and these files are then transferred to Unix OS.

Data processing for linkage analysis employing MLINK or Superlink

Data processing for linkage analysis employing Merlin or Allegro

License information

SNP HiTLink is provided free of charge. Copyright (c) 2008-2010 Shoji Tsuji, Yoko Fukuda and DYNACOM Co., Ltd. All rights reserved. If you are not willing to be bound by the terms and conditions of this License agreement, you can not use this software.

The software has been developed on the basis of research. The software shall not be liable for any losses or any direct, indirect, incidental, consequential, or other damages suffered by the licensee or others resulting from the use of the program or arising from any breach or warranty. The software may not be redistributed to a third party without the permission from Shoji Tsuji, Yoko Fukuda and DYNACOM Co., Ltd.

If you use SNP HiTLink in your work, please quote this publication.
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Fukuda Y, Nakahara Y, Date H, Takahashi Y, Goto J, Miyashita A, Kuwano R, Adachi H, Nakamura E, Tsuji S.
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data. BMC Bioinformatics. 2009 Apr 24;10(1):121.
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Download

SNP HiTLink Ver.1.5.1

User's manual (PDF version)

File Name	Release date
Manual.pdf	April 7, 2010

LD data (These files contain all data of D' and r2 of four ethnic population available from hapmap database.)

File Name	Description	Release date
hapmap_ld_CEU_20060614.zip	LD data for the CEU population.	November 18, 2008
hapmap_ld_CHB_20060614.zip	LD data for the CHB population.	November 18, 2008
hapmap_ld_JPT_20060614.zip	LD data for the JPT population.	November 18, 2008
hapmap_ld_YRI_20060614.zip	LD data for the YRI population.	November 18, 2008

System requirements

The following systems are required for SNP HiTLink.

Operating system: Windows XP SP2 or later / Vista (Use only 32-bit versions of Windows) and unix (supporting perl5) OS.
Other softwares: MLINK, Superlink, Merlin and Allegro should be installed in unix OS. Mlink is included in FASTLINK package. Allegro is available from deCODE genetics, Inc.

Version history

v1.5.1 (May 10, 2010)

a decimal point problem is fixed.

v1.5.0 (April 7, 2010)

Support the data from Illumina chip.

v1.2.0 (May 13, 2009)

Some bugs are fixed.
Speed up some analysis functions.

v1.1.0 (March 19, 2009)

Supports linkage analysis program Superlink and Merlin.

v1.0.0 (Dec 24, 2008)

Supports Affymetrix Mapping 100k/500k array set and Genome-Wide Human SNP array 6.0.
Supports linkage analysis program MLINK and Allegro.

Fukuda Y, Nakahara Y, Date H, Takahashi Y, Goto J, Miyashita A, Kuwano R, Adachi H, Nakamura E, Tsuji S. SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data. BMC Bioinformatics. 2009 Apr 24;10(1):121.
Dick Krueger KA, Tsuji S, Fukuda Y, Takahashi Y, Goto J, Mitsui J, Ishiura H, Dalton JC, Miller MB, Day JD, Ranum LPW. SNP Haplotype Mapping in a Small ALS Family. PLoS ONE. 4:e5687, 2009.

Contact information

Please send your comments and bug reports to snphitlink-admin(at)umin.ac.jp.
If you have any questions about this website, please contact us at info(at)dynacom.co.jp.
(Please replace (at) with @.)

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