VCF Imputation

The impute-nf pipeline subsets isotype reference strains from a hard-filter vcf file, creates a SNV-only VCF, and imputes a new VCF. This step is required for fine-mapping with NemaScan.

This page details how to run the pipeline.

Pipeline overview


        ##########                     #                    ##
            ##                       #####                 #  #
            ##                         #                   #
            ##    # ## ##  ###  #   #  #   ##       # ##  ####
            ##     #  #  # #  # #   #  #  #  #  ###  #  #  #
            ##     #  #  # #  # #   #  #  ###        #  #  #
            ##     #  #  # #  # #   #  #  #          #  #  #
        ########## #  #  # ###   ###   #   ###       #  #  #
                           #
                           #
                           #

    parameters                 description                                              Set/Default
    ==========                 ===========                                              ========================
    --debug                    Set to 'true' to test                                    (optional)
    --species                  Species: 'c_elegans', 'c_tropicalis' or 'c_briggsae'     (required)
    --vcf                      hard filtered vcf to calculate variant density           (required)
    --out                      output folder name                                       (optional)
    --chrI | chrII | chrIII... Window and overlap for each chromosome                   (optional)

Software Requirements

  • The latest update requires Nextflow version 24+. On Rockfish, you can access this version by loading the nf24_env conda environment prior to running the pipeline command:
module load python/anaconda
source activate /data/eande106/software/conda_envs/nf24_env

Relevant Docker Images

Note: Before 20220301, this pipeline was run using existing conda environments on QUEST and a script. However, these have since been migrated to docker images to allow for better control and reproducibility across platforms. If you need to access the conda version, you can always find the script from an old commit of the dry guide prior to 20210827

  • andersenlab/beagle (link): Docker image is created within this pipeline using GitHub actions. Whenever a change is made to env/beagle.Dockerfile or .github/workflows/build_beagle_docker.yml GitHub actions will create a new docker image and push if successful

Important

Make sure that you have gone through the Nextflow setup before running this workflow. `

Note

If you need to work with the docker container, you will need to create an interactive session as singularity can't be run on Rockfish login nodes.

interact -n1 -pexpress module load singularity singularity shell [--bind local_dir:container_dir] /vast/eande106/singularity/<image_name>

Usage

Note: if you are having issues running Nextflow or need reminders, check out the Nextflow page.

Testing on Rockfish

This command uses a test dataset

nextflow run -latest andersenlab/impute-nf --debug

Running on Rockfish

You should run this in a screen or tmux session.

nextflow run -latest andersenlab/impute-nf --vcf <path_to_vcf> --species <species>

Parameters

-profile

There are three configuration profiles for this pipeline.

  • rockfish - Used for running on Rockfish (default).
  • quest - Used for running on Quest.
  • local - Used for local development.

Note

If you forget to add a -profile, the rockfish profile will be chosen as default

--debug

You should use --debug for testing/debugging purposes. This will run the debug test set (located in the test_data folder).

For example:

nextflow run -latest andersenlab/impute-nf --debug

--species

Options: c_elegans, c_briggsae, or c_tropicalis

--vcf

Path to the hard-filtered vcf output from wi-gatk. VCF should contain ALL strains.

--chrI|chrII|chrIII|chrIV|chrV|chrX|MtDNA (optional)

The window size and overlap to use as inputs to Beagle. These parameters have been checked and decided on by previous lab members and Erik. Some chromosomes might require a window size of 3 and an overlap of 1. In recent conversation with the person who manages Beagle, they mentioned we should probably use default values unless we have done simulations to show these values are better. Note for the future maybe.

--out (optional)

default - impute-YYYYMMDD

A directory in which to output results. If you have set --debug, the default output directory will be impute-YYYYMMDD-debug.

Output

└── variation
    ├── WI.20240718.hard-filter.isotype.SNV.vcf.gz
    ├── WI.20240718.hard-filter.isotype.SNV.vcf.gz.tbi
    ├── WI.20240718.impute.isotype.SNV.vcf.gz
    └── WI.20240718.impute.isotype.SNV.vcf.gz.tbi