This pipeline is designed for human data, following the latest GATK Best Practices as of April 9, 2024. For the annotation part, we are using ANNOVAR. For Pathogenicity classification, we combined the results from InterVar and Tapes.

• Singularity
• Any human data files

• Please change the paths in the "Creating our directories" step of the script according to your directory.
• InterVar and Tapes were not installed in the singularity container due to configuration adjustments for the latest databases. Refer to their GitHub for installation procedures.
• To build your container simply run the following command:

  singularity build -f container.sif var_cont.def
  

• To test the container, try running any tool. For example, to run Samtools, use the following command:

  singularity exec -f container.sif samtools
  

• var_cont.def: Def file for creating the singularity container.

• variant_analysis.sh: The entire detailed code used for Variant analysis + Annotation + Identifying pathogenic variants.