GPHA CLIMB SARs-CoV-2 Lineage Line List

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Table of Contents

• GPHA CLIMB SARs-CoV-2 Lineage Line List
  • Table of Contents
  • Overview
  • Requirements
  • Installation
  • Usage
  • Config settings
    • Global params
    • Recent reporting window
    • Full reporting window
  • Troubleshooting

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Overview

This repo contains code to generate the covid linelist and lineage groupings.

Requirements

Data from the SARS-CoV-2 pipeline is sent by Core bioinformatics to an SFTP server.

Access is by service desk request.

Installation

Clone repo:

## clone the repo
git clone https://github.com/ukhsa-collaboration/gpha-climb-sars-cov2-lineage-line-list.git
## change into the directory
cd gpha-climb-sars-cov2-lineage-line-list
## create conda environment
## need python 3.12 or newer
conda create -n linelist_env python=3.12
## activate environment
conda activate linelist_env

User installation:

pip install .

Developer installation:

pip install -e ".[dev]"

Usage

## get latest data from the SFTP
get_data_covid_linelist --username forename.surname@ukhsa.gov.uk --outdir /path/to/output/dir/

## Refer to SOP for intermediate steps

## run the linelist
run_linelist --input /path/to/combined_pangolin_results.csv --output /path/to/results/folder/

Config settings

Global params

Global params are parameters that influence how the overall code runs or are used in both the recent and full reporting window.

Parameter	Description
period_size	Size of period to break the reporting window into in days. Currently set to 14 (2 weeks).
defined_variant	Not yet populated. Contains list of previously defined lineages to protect from collapsing/collapse no further than.

Recent reporting window

Recent reporting window refers to the period of time in which percentage based lineage prevalence is calculated. The recent reporting window is split into reporting periods (defined in global params as period_size) and a lineage must reach the percentage prevalence threshold in at least one of those periods to be protected in lineage grouping.

Parameters relating to the initial reporting window:

Parameter	Description
max_lineages	Maximum number of lineages to be protected. If more than max_lineages are identified to protect based on prevalence, these will be collapsed until max_lineages is reached.
min_lineages	Minimum number of lineages to be protected. If less than min_lineages are identified to protect based on prevalence, lineages will be collapsed until at least min_lineages are identified to protect.
weeks_to_include	Number of weeks to include in the recent reporting period.
percent_prevalence	Percent prevalence a lineage must reach to be protected.

Full reporting window

Full reporting window refers to the total period of time to include samples from, excluding samples falling in the initial reporting window. The number of most prevalent lineages to include from the full reporting period is calculated as the max_lineages value for the full reporting window minus the number of lineages identified to protect in the recent reporting window. As a minimum, an additional two lineages should always be protected in the full reporting window to account for lineages that had high prevalence previously that have since decreased.

Parameters relating to the full reporting window:

Parameter	Description
weeks_to_include	Number of weeks to include in the full reporting period.
max_lineages	Maximum number of lineages to be protected.

Troubleshooting