example_pipelines

Example Pipelines With the Sentieon tools

Example Sentieon pipelines implemented in shell script. You may modify these pipelines to work with your existing bioinformatics infrastructure.

See Sentieon's Argument Correspondence application note for information on how parameters in the Sentieon tools correspond to parameters in the GATK.

Example pipelines

• Germline variant calling
  • whole-genome sequencing - Standard germline variant calling suitable for whole-genome samples.
  • whole-genome sequencing with DNAscope - Higher accuracy germline variant calling for whole-genome samples.
  • whole-exome sequencing - Standard germline variant calling pipeline across target intervals.
  • whole-exome sequencing with DNAscope - Higher accuracy germline variant calling for whole-exome samples.
  • multiple input fastq - Standard germline variant calling pipeline, modified to support multiple pirrs of input FASTQ files.
  • joint calling - Standard germline variant calling pipeline with joint genotyping of multiple samples.
  • CCDG/functional equivalence pipeline - A Centers for Common Disease Genomics (CCDG) functional equivalent pipeline implemented in the Sentieon tools. See Sentieon's Functional Equivalent Pipeline application note for more information.
  • RNAseq - Germline variant calling from aligned RNAseq data. See the Sentieon manual for more information on this pipeline.
• Somatic variant calling
  • TNscope - Improved accuracy somatic variant calling.
    • default - Standard somatic variant calling with TNscope.
    • ml-model - TNscope somatic variant calling using a machine learning model.
    • amplicon - Somatic variant calling from amplicon data using a matched normal sample.
    • ctDNA - Somatic variant calling from cfDNA tumor-only samples.
    • ctDNA with UMI - Somatic variant calling from cfDNA tumor-only samples with UMI-tagged reads.
    • target capture - Somatic variant calling from hybridization catpure data using a matched normal sample.
  • TNseq - Pipelines matching best practice implementations for somatic variant calling.
    • tumor-normal - Somatic variant calling with TNsnv and TNhaplotyper from paired tumor-normal samples.
    • tumor-only - Somatic variant calling with TNsnv and TNhaplotyper from tumor-only samples.