Overview - SNV Somatic
The CGAP Pipelines module for somatic Single Nucleotide Variants (SNVs) (https://github.com/dbmi-bgm/cgap-pipeline-SNV-somatic) is our solution to filter and annotate the variants called by CGAP Somatic Sentieon module.
The input vcf contains SNVs, short Insertions and Deletions (INDELs), and Structural Variants (SVs), which are filtered, annotated and reformatted for use in the somatic browser.
Docker Image
The Dockerfiles provided in this GitHub repository can be used to build public docker images.
If built through portal-pipeline-utils pipeline_deploy command (https://github.com/dbmi-bgm/portal-pipeline-utils), private ECR images will be created for the target AWS account.
The image contains (but is not limited to) the following software packages:
- vcftools (954e607)
- granite (0.2.0)