This workflow is for imputation using low coverage whole genome sequencing data with QUILT. Also, it can perform benchmarking for both QUILTs and GLIMPSEs given different scenarios.
- QUILT2 (QUILT_prepare_reference.R, QUILT.R)
- GLIMPSE v2.0 (GLIMPSE2_split_reference, GLIMPSE2_phase, GLIMPSE2_ligate)
- GLIMPSE v1.1.1 (GLIMPSE_chunk, GLIMPSE_phase, GLIMPSE_ligate)
- samtools
- bcftools
- vcfppR
git clone https://github.com/Zilong-Li/lcWGS-imputation-workflow
cd .test && ln -s ../workflow
snakemake -j10 -n
The usage of this workflow is described in the Snakemake Workflow Catalog.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) https://github.com/Zilong-Li/lcWGS-imputation-workflow and its DOI (see above).