yr542/variant_identification_application_via repository overview

⁠Mendelian Variant Identification Application (VIA) Version 2:

⁠Basic Information:

VIA (Variant Identification Application) automates the process of variant identification, analyzing family data and returning possible candidates based on a range of specific filters and models of inheritance for mendelian varients.

• This docker uses the Github referred to the yr542/Variant_Identification_Applicaton___VIA___V2⁠.
• It includes minor updates and modifications to the original Dockerfile.
• We generally pull our docker as a singularity/apptainer. The run commands we used here use apptainer.
• Please refer to the main README in the linked GitHub repository for details on required input files.
• VIA is currently being integrated into an in-house Nextflow pipeline developed by Dr. Isabelle Schrauwen’s laboratory, focused exclusively on Mendelian (non-complex) genetic disorders. This pipeline is freely shared with collaborators.
• The Docker container can be run independently of the Nextflow pipeline. As it's input requirements can be quite intensive to create.
• This image includes all development versions of the Docker container (except the first one), whereas only the most stable versions are published to the GitHub container registry.

⁠Script Related Variables Used:

• Please refer to the Mendelian variant VIA Version 2 Github repository for more information.

## Output File Path
output_file="/path/to/my/MyVIAprocessedBatch.csv"
## Path to filtered phen file:
output_filted_phen=""

## Path to the post processed output from mendelian filtration
mendelian_step_output="/path/to/the/output/of/mendelian/post/processed/MyPostProcessedFile.txt"
### A pedigree file
pedigree_file="/path/to/batch/pedigree/file/MyBatch_Pedigree.txt"
### A phenotype file
phenotype_file="/path/to/the/MyBatch_Phen.txt"

## An HPO phenotype to genes file
hpo_mapping_file="/path/to/phenotype_to_genes_new_modified.txt"


## The apptainer image
apptainer_image="/path/to/your.sif"

⁠Version Specific Information

⁠Version 10 (Micromamba)

• This uses the command VIA that knows where the main.py is.
• Due to the wrapper script the filted phen file path needs to be given
• To run use the command:

apptainer exec \
  --bind "$(dirname "$mendelian_step_output")" \
  --bind "$(dirname "$phenotype_file")" \
  --bind "$(dirname "$output_file")" \
  --bind "$(dirname "$pedigree_file")" \
  "$apptainer_image" VIA \
    --pedfile "$pedigree_file" \
    --data "$mendelian_step_output" \
    --output "$output_file" \
    --phenfile "$phenotype_file" \
    --mapfile "$hpo_mapping_file" \
    --output_phen "$output_filted_phen"

⁠Versions 7 and 9 (Miniconda):

Version 7 and 9 are the most stable miniconda versions. Version 9 is much smaller than version 7. They use an entrypoint.sh script to run to activate their internal required miniconda environment.

• If this docker is pulled as a Singularity it is important to note that all Python scripts are located in the /via directory.
• Unlike the micromamba version the output path for the filtered phen file does not have to be specified.

Uses the command to run:

apptainer exec \
  --bind "$(dirname "$mendelian_step_output")" \
  --bind "$(dirname "$phenotype_file")" \
  --bind "$(dirname "$output_file")" \
  --bind "$(dirname "$pedigree_file")" \
  "$apptainer_image" /entrypoint.sh python /via/main.py \
    --pedfile "$pedigree_file" \
    --data "$mendelian_step_output" \
    --output "$output_file" \
    --phenfile "$phenotype_file" \
    --mapfile "$hpo_mapping_file"