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Snakemake workflow: lcWGS-imputation-workflow

Snakemake

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.

Dependencies

  • 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

Quick start

git clone https://github.com/Zilong-Li/lcWGS-imputation-workflow
cd .test && ln -s ../workflow
snakemake -j10 -n

Usage

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).

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Imputation workflow for low coverage whole genome sequencing data

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