/snv_analysis_pipeline

Workflow for post-processing of Somatypus variants

Primary LanguageR

snv_analysis_pipeline

Summary

This pipeline is part of the nuclear horizontal transfer in CTVT project.

It's used for post-processing of Somatypus variant calls. This pipeline does various things, including:

  • Separating germline and somatic variants
  • Running some filters on the data (described in the paper)
  • Annotating the variants using Variant Effect Predictor
  • Making a phylogenetic tree of the samples

Dependencies

I've containerised the software dependencies. Three containers are needed in total: snv_analysis_pipeline.sif, vep_104.sif and somatypus-dev.sif. TODO: Add instructions on how to build/download these containers.

Nextflow config

The nextflow.config file given is for illustration purposes only. It's tuned for the compute farm at the Sanger. It will need to be modified for other platforms.