VCF Genotype Search¶
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.
Note
The following feature is currently being developed. Please access it at https://dev.plantinformatics.io/login using the following login credentials. Username: test@test Password: test
Loading a VCF and selecting samples¶
Click on the Search tab in the left navigation panel.
While in the search tab, find the VCF Genotype Search box.
Within the box, select your VCF to search.
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.
(Optional) Loading multiple samples¶
Note
The following search has only been tested up to 1000 samples. The interface will become extremely slow if a larger number of samples are selected. If it does become slow efresh the page to restart.
To select a range of samples, hold down the CRTL key and select another sample in the list.
Adding features to be searched¶
Within the Features input text box, paste your feature IDs. The one used in this example is:
AVRIG00246
AVRIG00484