Software Manual for Sentieon Genomics pipeline tools

Sentieon develops and supplies a suite of bioinformatics secondary analysis tools that process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy, and 100% consistency.

You could also download the PDF version here Sentieon Manual

Sentieon Manual

• 1. Introduction
  • 1.1. Description
  • 1.2. Benefits and Value
  • 1.3. Platform Requirements
  • 1.4. Installation procedure for a Linux Based system
  • 1.5. Installation procedure for an Apple OSX system
  • 1.6. Useful environmental variables when using the software
  • 1.7. Keywords
• 2. Typical usage for DNAseq
  • 2.1. General
  • 2.2. Step by step usage for DNAseq
• 3. Typical usage for DNAscope
  • 3.1. General
  • 3.2. Step by step usage
• 4. Typical usage for TNseq
  • 4.1. General
  • 4.2. Step by step usage
• 5. Typical usage for TNscope
  • 5.1. General
  • 5.2. Step by step usage
• 6. Typical usage for RNA variant calling
  • 6.1. General
  • 6.2. Step by step usage
• 7. Detailed usage of the tools
  • 7.1. DRIVER binary
  • 7.2. TNHAPFILTER script
  • 7.3. BWA binary
  • 7.4. UTIL binary
  • 7.5. UMI script
  • 7.6. PLOT script
  • 7.7. LICSRVR binary
  • 7.8. LICCLNT binary
• 8. Examples of tool capabilities and applications
  • 8.1. DNA pipeline example script
  • 8.2. Working with multiple input files
  • 8.3. Supported annotations in Haplotyper and Genotyper
  • 8.4. Removing reads after alignment with low mapping quality
  • 8.5. Performing Dedup to mark primary and non-primary reads
  • 8.6. Pipeline modifications when using data with quantized quality scores
  • 8.7. Modify RG information on BAM files when both Tumor and Normal inputs have the same RGID
  • 8.8. Running the license server (LICSRVR) as a system service

Appendix

• Troubleshooting
  • Preparing reference file for use
  • Preparing RefSeq file for use
  • Common usage problems
  • KPNS - Known Problems No Solutions
• Release notes and usage changes
  • Updates from previous releases
  • Usage changes from previous release

• Acknowledgements
• Acronyms and Abbreviations
• Disclaimer