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Creating a summary of accessions for a known set of SNPs

In this Use Case, a summary of genotypes for AGG Plant Genetic Resources can be simply and rapidly visualised. For example, a user may wish to view the genotypes for a set of accessions of interest at a small subset of trait linked markers, to make a decision on which accessions to use in an experiment. In this example we will use Pretzel to display a summary of a set of AGG barley Plant Genetic Resources at two markers AVRIG00246 and AVRIG00484.

vcf-feature-search

Loading a VCF and selecting samples

Click on the Search tab in the left navigation panel. vcf-feature-search-01 While in the search tab, find the VCF Genotype Search box. Within the box, select your VCF to search. vcf-feature-search-02 This will load the VCF and give you a list of all the available samples. If one is clicked it will automatically be added into selected samples input box. vcf-feature-search-03

(Optional) Loading multiple samples

Note

It is recommended to only select a small number of samples (up to 1000). The interface may become unresponsive if a larger number of samples are selected. If it does become slow refresh the page to restart.

Should there be a need for a large number of samples (>1000), please don't hesitate to contact us.

To select a range of samples, hold down the CRTL key and select another sample in the list. vcf-feature-search-04

Adding features to be searched

Within the Features input text box, paste your feature IDs. The one used in this example is:

Feature names
AVRIG00246
AVRIG00484
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End output

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(Optional) Selecting additional features from the view

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