This script generates flanking sequence for variants listed in https://github.com/phe-genomics/variant_definitions.
Download and unpack or clone this repo, which includes the variants2probes.pl perl script plus a copy of the wuhan_hu-1.fa reference sequence
To run on a mac or unix system, type ./variants2probes.pl
This will produce output summary files in several different formats including variant_probe_matrix.txt, an example of which is included in this folder.
On a system without wget, you could manually download and unpack the variant data from https://github.com/phe-genomics/variant_definitions/archive/refs/heads/main.zip. Be sure that the yaml files for each variant are in the subdirectory variant_definitions-main/variant_yaml relative to your present working directory.
The use of this script depends on the format of the yml files from phe-genomics remaining unchanged. Get in touch if you have any problems.