Sentieon® documentation
Welcome to the Sentieon® documentation!
- Download the complete documentation as a PDF here:
Example Usage
- Typical usage for Pangenome
- Typical usage for DNAseq®
- Typical usage for DNAscope
- Typical usage for TNseq®
- Typical usage for TNscope®
- Typical usage for RNA variant calling
- Examples of tool capabilities and applications
- DNA pipeline example script
- Working with multiple input files
- Supported annotations in Haplotyper and Genotyper
- Removing reads after alignment with low mapping quality
- Performing Dedup to mark primary and non-primary reads
- Pipeline modifications when using data with quantized quality scores
- Modify RG information on BAM files when both Tumor and Normal inputs have the same RGID
- Running the license server (LICSRVR) as a system service
Advanced Usage
- Sentieon-cli
- Deduplication and UMI Handling
- Somatic Variant Calling for SNPs and Indels
- Sentieon Application Notes
- Arguments Correspondence
- Deployment Guide for Amazon Web Services
- Deployment Guide for Azure
- Germline Copy Number Variant Calling for Whole-Genome-Sequencing with CNVscope
- Distributed Mode
- Functional Equivalent Pipeline from CCDG using Sentieon®
- Building and Installing gnuplot
- Using jemalloc to Optimize Memory Allocation
- License Server Extension
- Description of output files and fields
- Recommendations on Read Groups
User Manual
Appendix