https://github.com/danko-lab/glimpse2_setup
Scripts to create a phased reference panel from 1kGP for imputation with GLIMPSE
https://github.com/danko-lab/glimpse2_setup
Last synced: 10 months ago
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Scripts to create a phased reference panel from 1kGP for imputation with GLIMPSE
- Host: GitHub
- URL: https://github.com/danko-lab/glimpse2_setup
- Owner: Danko-Lab
- License: mit
- Created: 2023-06-24T12:27:07.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-05T18:12:40.000Z (about 2 years ago)
- Last Synced: 2024-05-05T19:27:31.585Z (about 2 years ago)
- Language: Python
- Size: 13.7 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# GLIMPSE2_setup
This repo contains a snakemake pipeline to create a phased reference panel from 1kGP for imputation with GLIMPSE2. This pipeline follows their [tutorial](https://odelaneau.github.io/GLIMPSE/docs/tutorials/getting_started/#3-split-the-genome-into-chunks) and use the most recent high coverage integrated phased panel from [1kGP](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/).
## Requirements
Software requirements are detailed in the conda environment file (`spec/snakemake.yml`). Paths to the base directory where everything will be downloaded/written and to GLIMPSE should be set by editing `spec/file_spec.json` (by default, this will be written to a subdirectory `outputs` where this repo is downloaded). GLIMPSE uses genetic maps to help decide how to chunk the genome to. The install path for GLIMPSE and parallel must be provided in the spec file.
Note that the X chromosome is bugged, and I have not yet figured out how to fix it. For now, I am just excluding it entirely (both non-PAR and the two PARs).