Overview - Sentieon Joint Calling
The CGAP Pipelines module for joint calling and genotyping with Sentieon (https://github.com/dbmi-bgm/cgap-pipeline-upstream-sentieon) accepts multiple individual g.vcf files and produces a jointly genotyped vcf file as output.
The g.vcf files can be generated through standard CGAP Pipelines processing (either of the CGAP Upstream modules followed by HaplotypeCaller) or can be provided by the user.
This pipeline is based on Sentieon and the GVCFtyper algorithm is used to combine the g.vcf files and joint genotype the resulting variants.
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:
- sentieon (202112.01)
