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Haploview how to carry out chain imbalance analysis, many novices are not very clear about this, in order to help you solve this problem, the following editor will explain for you in detail, people with this need can come to learn, I hope you can gain something.

Haploview is a software based on graphical interface, which is well designed and easy to use, so it is one of the mainstream software for linkage disequilibrium analysis.

You need two input files with suffixes of ped and info. The ped file saves the genotyping results of the sample, which is described in detail in the previous article; the info file stores the ID and location information of the SNP locus, as follows

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The first is the ID of the SNP locus, and the second is the location of the SNP locus in the genome.

1. Import input Fil

Click the Linkage Format menu, and then select the corresponding input file. Data File specifies the input ped file, and Locus Information File specifies the output info file. If the ped file and the info file have the same name, the program will automatically recognize the info file while specifying Data File. Ignore pairwise comparisons of markers specifies the range for calculating LD. By default, only the SNP loci within the distance of 500kb are analyzed for linkage imbalance, which can be adjusted according to your own needs. For example, the sample is filtered to 1000KB individuals, and the samples with default genotype deletion greater than 50% are removed. When all the parameters are set, click the OK button.

two。 Filter the input SNP loci

Check markers can filter the input SNP sites according to the thresholds of HW pvalue, Min genotype, mendel error, MAF and so on. After setting the corresponding threshold, click the Rescore Markers button to filter according to the threshold. If the Rating in the last column is checked, it means that the SNP site meets the requirements.

3. LD plot

Click the LD plot button to see a heat map of the linkage disequilibrium shown below; each grid represents the results of LD analysis between two SNP loci, with colors ranging from white to red, representing low to high linkage levels. Right-click on the grid to see the detailed results of the LD analysis. The value in the box is the D' value, which is multiplied by 100 for beauty. The appearance of the heat map can be adjusted through the top Display button.

Highly linked SNP sites make up haplotype block. For example, 1-8 in the figure below make up block1, which is 84kb in length.

4. Haplotypes

Based on the results of LD analysis, you can define a haplotype block. Through the top Analysis button, you can adjust the algorithm for calculating haplotype block

5. Tagger

The Tagger button is used to select tagSNPs. Configuration has two uses. The first is to filter SNP sites. By checking the corresponding checkbox, you can specify the SNP sites you want to analyze. The second use is to specify the algorithm for tagSNPs selection. The default is pairwise tagging only.

Once set up, click the Run Ragger button, and the resulting interface is as follows

What is displayed in the Test box is the selected tagSNPs. Click each SNP site with the left mouse button, and in the Alleles captued by Current Selection box below, the other SNP sites represented by the tagSNP will be displayed. The table on the right shows the best tagSNP for each SNP site. The results can be exported through the Dump Tests File and Dump Tags File buttons below.

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