Introduction

UCL-BLIC/ENGI-exoseq is a bioinformatics analysis pipeline that performs best-practice analysis pipeline for Exome Sequencing data.

The pipeline is built based on GATK best practices using Nextflow, a bioinformatics workflow tool. The main steps done by pipeline are the following (more information about the processes can be found here).

• Alignment
• Marking Duplicates
• Recalibration
• Realignment
• Variant Calling
• Variant Filtration
• Variant Evaluation
• Variant Annotation

Documentation

The UCL-BLIC/NGI-exoseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Pipeline installation and configuration instructions
2. Running the pipeline
   • Preparing custom exome capture kits
3. Output and how to interpret the results
4. Troubleshooting