Find Samples and Genotype from selected haplotype

[Don-Isdale]

Introduction

A recurrent work-flow in the User Stories 2 and 3 is to select a number of samples and then click on SNPs to sort the displayed samples by their genotype values at those SNPs. This enables the user to identify a haplotype using Genotype values, i..e Alt / Ref, at those SNPs and find samples which have the chosen haplotype .

This operation sorts the samples which are loaded into the frontend GUI, based on the Genotype values which are loaded in the frontend.
For a dataset with 300 samples this is fine, but with AGG datasets with 30000 samples, it becomes necessary to do this operation on the server ("backend") to effectively say how many samples in the collection have the identified haplotype, and retrieve their genotype values.

This issue discusses a proposed feature enabling this work-flow :

• after identifying the desired haplotype by selecting SNPs, and identifying Alt/Ref at each SNP, the user will be able to view the samples which have that haplotype
• the Genotype values can then be requested for these samples

GUI design

A simple way to trial this functionality is to add a button in the Genotype table control dialog which will narrow the list of available samples to just those which have the identified haplotype.
The user can the select some or all samples from this list, and proceed with the VCF Lookup request as in existing work-flows.

Design of lookup functionality on the server

The method of using vcftools to implement this will be based on specifying which SNPs have Alt and Ref, using bcftools --include with --regions (e.g. `bcftools view -e 'GT="0/0"' -r chr1:123456,chr2:7891011' as in this LLM answer.

Task Structure

The work breakdown is as follows :

• testing of bcftools commands on VCF files with large number of samples to gauge the performance of this function
• add the server endpoint which implements this function
• add the button which gets the list of samples and displays it on the available samples list

Each of these will be described and tracked by a sub-issue which will be a part of this issue.