Finding genotyped accessions carrying a specific haplotype

New feature in v3.7.3

• Added the ability to search a VCF file for accessions carrying a specific SNP or haplotype.
• Try out this few feature now on agg.plantinformatics.io - sign up for a free account now to get started!

This section assumes some working knowledge of using the Genotype tab

Introduction

In this example, we will search AGG wheat genotypes (Triticum aestivum - IWGSC_RefSeq_v2.1 - Genotypes - AGG Filled-in Release 1) for accessions carrying the Yr34/Yr48 haplotype located at the end of Chr5A.

For more information on how we found the accessions carrying Yr34/Yr48 where located at the end of Chr5A using Pretzel please see User Story 2.

Finding the VCF file

Start by adding the VCF file which contains all of the AGG wheat accessions that we will eventually search. This can be found using the search pannel on the left hand side of the screen and searching for agg wheat filled. This should help us find Triticum aestivum - IWGSC_RefSeq_v2.1 - Genotypes - AGG Filled-in Release 1.

Navigating to the region of interest

We are interested in the end of Chr5A, so open up dataset and load in Chr5A. Next, to want to navigate to the end of Chr5A. This can be done by clicking and dragging over the region of interest and pressing the zoom button that appears at the bottom. Then select the region again, making sure to cover up to the end of the chromosome. This is done to select the features we want to visualise. Next, open the Genotypes tab in the right panel, which displays the selected SNPs.

Selecting the haplotype

To add the haplotype we want to search, click on the specific allele located in the REF and ALT columns. If you made a mistake, you can click on the same allele again to de-select it.

Example specific information

To search for Yr34/Yr48, we can use the pattern identified already in User Story 2.

Filtering the accessions for the haplotype

Once the haplotype has been defined, open up the sample selection menu by clicking on the cog icon within the Genotypes tab and select the "Filter by defined haplotype" option. This will filter the accessions for only those that match the selected haplotype. This will then update the number of haplotypes and update the list of selectable accessions in the sample selection menu.

In this example, we see a change from AGG wheat 12,606 accessions (the full list of accessions in the file) to a filtered list of 333 accessions which match this exact haplotype.

Viewing and using the results

There are a couple of ways to view the results; the easiest is to display this within Pretzel. By going down to the accessions selection box click on the first accession, hold Shift then scroll down to the bottom of the list to select the last accession.

This should select all 333 of the filtered accessions. Then click VCF Search to load the genotypes for these accessions into the genotype table.

Exporting the results (optional)

There are two main ways to export the results of the search. The first is to export the genotype table as a VCF file. This can be done by clicking the VCF Download button above the genotype table.

The other way to export is within the accession selection menu. This can be done by clicking the copy to clipboard button. This will copy the list of accessions to the clipboard in a list.