Accessory software for dChipLinkage

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Accessory software for dChipLinkage

Manual

I. Create Folder/Directory for all programs and data. Let's call it Working Directory.

Download and extract files from archive to your Working Directory

It includes the following Perl programs:

_3_runALL.comb.win.pl, _3_runALL.GDAS.win.pl, _0_format_data.comb.win.pl, _0_format_data.GDAS.win.pl, _1_create_linkped.loci.win.pl, _11_cut_linkped.loci.win.pl, _12_fix_errors.win.pl, _13_pedcheck.err.win.pl, _2_Merlin2dChip.coml.win.pl, linkage2call-ped-info.pl;

the following data files:

EXAMPLE_call.xls, EXAMPLE_ped.xls, EXAMPLE_linkped.chr1, EXAMPLE_lincloci.chr1, README, three Info files, six data files in GDAS format;

and Graphical User Interface files:

VisualPerl.tar.gz, VisualPerl.rar, VisualPerlW.exe, visualperl.ini, win32api.dll.

To use accessory software you need to have Perl installed on your computer. Go to ActivePerl to download distribution of Perl, available for Windows, Linux and Solaris.

For Windows users, please follow the instructions below. For Linux/Unix users, please download Unix version of these programs.

You also need to download and unpack version of Merlin precompiled for Windows. Get it here. After unpacking folder "merlin-version#" will appear. Copy entire content of this folder to your Working Directory.

You also need to download and unpack Allegro executables. To get archive e-mail: allegro@decode.is . Folders "bin", "doc", "examples", "src", and several files will appear. Follow instructions from "INSTALL" file. To use Allegro, copy a precompiled version of Allegro (DOS) from the "bin" directory to your Working Directory.

Register and download precompiled version (Windows) of PedCheck from here. Place "pedcheck_win.exe" file to your Working Directory.

If you would like to use Graphical User Interface, Java Runtime Environment is to be downloaded and installed from here.

I. For Windows users, please uncompress VisualPerl.rar with Winrar. Assuming you uncompress the files to directory VisualPerl, then you can launch the GUI under that directory with command java -jar VisualPerl.jar (For Windows XP, you can run such commandline by clicking Start/Run, then type in cmd and press return key). Alternatively, you can choose to use the pseudo-executable file VisualPerl.exe instead and run it directly by clicking on it.

II. For Linux/Unix users, please uncompress VisualPerl.tar.gz with the following two commands:
(1) gunzip VisualPerl.tar.gz
a file VisualPerl.tar will be generated
(2) tar -xvf VisualPerl.tar
Assuming you uncompress the files under directory VisualPerl, then you can launch the GUI there with command java -jar VisualPerl.jar

II. Call two linkage analysis software (Merlin and Allegro) and produce curve files at once (recommended)

We recommend to convert text files containing SNP calls to Linkage format, remove all non-informative markers, detect and fix incompatibilities in pedigree data, call two linkage analysis software and produce curve files at once. If you would like to prepare files and to run software step by step go to section IV of this Manual.

You can use either Graphical User Interface, or to run programs from a command line.

Please note that by default the software use DOMINANT model! If you would like to change it to RECESSIVE one open the program '_1_create_linkped.loci.win.pl' in any text editor and follow instructions on line 305.

For GUI, please launch the GUI (see instructions above). In the window appeared under "Setting/Directory" browse for you Working and Perl System Directories, the press "Save". After that under "GetCurve/GetCurveMerlinAllegro" please browse for your Pedigree File (see EXAMPLE_ped.xls) and Genome Info File. Last file is one of Affymetrix information files created for three different ethnic groups (for example, 11k_genome_info_hg15_asian.xls). If your input file is single GDAS text file containing SNP genotype calls for each sample (see ONE.TXT) choose "I am using GDAS Format". If your input file is combine text file exported by Affymetrix software or dChip (see EXAMPLE_call.xls), choose "I am using Combined Format" and then browse for Combined Format File (see EXAMPLE_call.xls). Then press "Run".

Output files will contain 23 linkped and 23 linkpoci files for each dataset, Merlin and Allegro result files, and Curve.xls files ( Allegro-NPL, Allegro-LOD and Merlin) containing SNP ID, chromosome number, position (Mb), genetic distance (cM), and LOD score for each SNP.

For Command Line. Program “_3_runALL.comb.win.pl” should be used if input files are combined text file exported by Affymetrix software or dChip (see EXAMPLE_call.xls). This program is executed from a command line (or in TextPad window) followed by Call file (see EXAMPLE_call.xls), Pedigree file (see EXAMPLE_ped.xls) and Information file names. Last file is one of Affymetrix information files created for three different ethnic groups (for example, 11k_genome_info_hg15_asian.xls).

Example:

folder_name>_3_runALL.comb.win.pl EXAMPLE_call.xls EXAMPLE_ped.xls 11k_genome_info_hg15_asian.xls

Program “_3_runALL.GDAS.win.pl” should be used if input files are single GDAS text files containing SNP genotype calls for each sample (see ONE.TXT). This program is executed from a command line (or in TextPad window) followed by Pedigree file (see EXAMPLE_ped.xls) and Information file names. Last file is one of Affymetrix information files created for three different ethnic groups (for example, 11k_genome_info_hg15_asian.xls).

Example:

folder_name>_3_runALL.GDAS.win.pl EXAMPLE_ped.xls 11k_genome_info_hg15_asian.xls

III. Conversion Linkage format data files into dChip Call and Pedigree file format for analysis in dChip

You can use either Graphical User Interface, or to run programs from a command line.

For GUI, please launch the GUI (see instructions above). In the window appeared under "Setting/Directory" browse for you Working and Perl System Directories, the press "Save". After that under "Covert/Linkage->dChip" please browse for your Linkage Pedigree File (see EXAMPLE_linkped.chr1) and Linkage Loci File (see EXAMPLE_lincloci.chr1). Then press "Run".

Output files are “ped_name._call.xls”, “ped_name._ped.xls” and “ped_name._info.xls” identical to combined text files exported by Affymetrix software or dChip (see above).

For Command Line. Program “linkage2call-ped-info.exe” is converting Linkage format files to “_call.xls”, “_ped.xls” and “_info.xls” files then used for linkage analysis in dChip. Input files for this program are linkped and linkloci files (see EXAMPLE_linkped.chr1, EXAMPLE_lincloci.chr1). The program is executed from a command line followed by any one of linkped and linkloci file names.

Example:

folder_name>linkage2call-ped-info.pl linkped_file linkloci_file

Output files are “ped_name._call.xls”, “ped_name._ped.xls” and “ped_name._info.xls” identical to combined text files exported by Affymetrix software or dChip (see above).

IV. Prepare and modify files in Linkage Format, and call linkage analysis software by steps (you can do it at once, see section II)

1. Conversion of text files containing SNP calls to Linkage (Merlin/GeneHunter) format for analysis. The text file can be GDAS single text file for each sample, or a combined text file output by GDAS or dChip

Two programs should be used to convert files containing SNP calls to Linkage format files. Input files are either single GDAS text file containing SNP genotype calls for each sample, or a or a combined text file exported by Affymetrix software or dChip. Therefore, first program which are parsing input files and returning output files for each pedigree member named “ped_name.chrALL.txt” existing in two versions. The first version is “_0_format_data.GDAS.win.pl” and the second one is “_0_format_data.comb.win.pl”. Both versions are executed from a command line followed by Pedigree or Call file, and Information file names. Last file is one of Affymetrix information files created for three different ethnic groups.

Examples:

folder_name>_0_format_data.GDAS.win.pl ped_name 11k_genome_info_hg15_asian.xls

forder_name>_0_format_data.comb.win.pl file_name.call.xls 11k_genome_info_hg15_asian.xls

Output files from both versions are containing SNP_ID and Call columns. Second program, called “_1_create_linkped.loci.win.pl” is parsing pedigree info files and output files from the first program, and returning separate linkped and linkloci files for each chromosome in Linkage format. Allele frequencies are calculated based on actual genotype data for this pedigree. The program is also executed from a command line followed by Pedigree and Information file names.

Please note that by default the program uses DOMINANT model! If you would like to change it to RECESSIVE one open the program '_1_create_linkped.loci.win.pl' in any text editor and follow instructions on line 305.

Example:

folder_name>_1_create_linkped.loci.win.pl ped_name 11k_genome_info_hg15_asian.xls

2. Running Linkage Analysis Software

Proceed according to the manual of specific program.

Questions or problems regarding this web site should be directed to Igor Leykin