Data retrieval: Formats - Haploview
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This section generates a properly formatted and ready-to-use file that you can use as an input file for the Haploview software:



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The procedure that one needs to follow depends of the type of Haploview file that you want to generate:

Linkage Format

1. Enter a Description to identify the process.

2. Select which of the SNPs in your Study are going to be used. You can do it in several ways:

- By position: You can specify a chromosome and a begin and end positions which delimit a region you are interested in.

- By Region: Depending on the content of the field "Region" in your SNPs Table.

- By Gene: Depending on the content of the field "Gene" in your SNPs Table.

- ALL: All SNPs will be selected.

3. Click the "Linkage Format" button.

Information about sex and affection of samples has to be provided in order to create a linkage format file. Therefore, a new form appears where this can be done:

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4. In the sex definition boxes, just introduce values defining sex as they are in the "sex" field of the Samples Table.

5. In the Case/Control boxes,

- Select the field of the Samples Table that defines cases and controls:

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- Then you need to select the proper values for cases and controls:
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Samples with values other than the ones declared here will be discarded and not used in the process.

When more than two possible values exist in a field. You may want to enter only one of those values in either the "Case" or the "Control" boxes, leaving the other box untouched (that is, leaving the "[Select Item]" option there). By doing so, those samples that match your explicit selection are being defined as, say, Cases (or Controls, if you selected so). All the remaining samples having other values will be used as Controls.

If a blank is selected " ", that means that there are Samples with no value in the field and that those are being selected as a case or control.

6. The "Retrieve Data" button has to be pressed and the resulting file will appear in the User results section.

There should be a *.zip file containing:

- snps.txt
List of SNPs with their positions in the format required by Haploview

- linkageFormatHaploviewReport.txt
The input file for Haploview with the genotype information in linkage format.

- information.txt
SNPator information to identify the job: date, time, user, study and filter.

Pseudo Phased Haplotypes

The file is generated from the genotypes information and, thus, phase  is not known or assumed. Heterozygous genotypes will be marked with the letter "h".


1. Enter a Description to identify the process.

2. Select which of the SNPs in your Study are going to be used. You can do it in several ways:

- By position: You can specify a chromosome and a start and end positions which delimit a region you are interested in.

- By Region: Depending on the content of the field "Region" in your SNPs Table.

- By Gene: Depending on the content of the field "Gene" in your SNPs Table.

- ALL: All SNPs will be selected.

3. Click the "Pseudo Phased Haplotypes" button. The resulting file can be found in the User Results section.

There should be a *.zip file containing:

- snps.txt
List of SNPs with their positions in the format required by Haploview

- pseudoPhasedFormatHaploviewReport.txt
The input file for Haploview with genotype information.

- information.txt
SNPator information to identify the job: date, time, user, study and filter.

Phased Haplotypes

The Haploview file will be generated from a previously run PHASE haplotype estimate and, consequently, with known genetic phase.

1. Enter a Description to identify the process.

2. Select a previously run PHASE result in the "User results" combobox

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3. Press the "Phased Haplotypes" button. The resulting file can be found in the User Results section.

There should be a *.zip file containing:

- snps.txt
List of SNPs with their positions in the format required by Haploview

- phasedFormatHaploviewReport.txt
The input file for Haploview with the genotype information.

- information.txt
SNPator information to identify the job: date, time, user, study and filter.

- Haploid data treatment.

Currently, only diploid genotypes are being supported.