Overview of the pipeline

Here is a brief overview of the entire pipeline. For details see subsections and the hydra-genetics documentation.

DNA (FFPE)

dag plot

  1. Input files: fastq
  2. Downsample: seqtk
  3. Trimming using fastp
  4. Alignment using BWA-mem
  5. Mark duplicates using Picard
  6. SNV and INDEL
    6.1 Calling using Mutect2 and Vardict
    6.2 Annotation using VEP and hydra-genetics annotation module 6.3 Filtering using bcftools and hydra-genetics filtering module
  7. CNV
    7.1 Calling using CNVkit, GATK CNV and Jumble 7.2 Merging using SVDB 7.3 Annotation using SVDB and hydra-genetics
    7.4 Filtering using hydra-genetics
    7.5 CNV html report using hydra-genetics filtering module
  8. Fusion calling using FuSeq_WES and JuLI
  9. Biomarkers
    9.1 TMB using hydra-genetics biomarker module 9.2 MSI score using MSIsensor-Pro
    9.3 HRD using CNVkit/ScarHRD and Jumble
  10. QC
    10.1 QC measures from Samtools, Picard, FastQC, GATK
    10.2 MultiQC hmtl report
    10.3 Hotspot coverage report
    10.4 Sample mixup check

DNA (ctDNA)

dag plot

  1. Input files: fastq
  2. Downsample: seqtk
  3. Trimming using fastp
  4. Alignment using BWA-mem and UMI consensus calling
  5. SNV and INDEL
    5.1 Calling using Mutect2 and Vardict
    5.2 Annotation using VEP and hydra-genetics annotation module 5.3 Filtering using bcftools and hydra-genetics filtering module
  6. CNV
    6.1 Calling using CNVkit, GATK CNV and Jumble 6.2 Merging using SVDB 6.3 Annotation using SVDB and hydra-genetics
    6.4 Filtering using hydra-genetics
    6.5 CNV html report using hydra-genetics filtering module
  7. Fusion calling using JuLI
  8. Biomarkers
    8.1 TMB using hydra-genetics biomarker module 8.2 MSI score using MSIsensor-Pro 8.3 HRD using Jumble
  9. Fragmentomics using FinaleToolkit
  10. QC
    10.1 QC measures from Samtools, Picard, FastQC, GATK
    10.2 MultiQC hmtl report
    10.3 Hotspot coverage report

RNA

dag plot

  1. Input files: fastq
  2. Downsample: seqtk
  3. Alignment using Star
  4. Fusions
    4.1 Fusion calling using Arriba, StarFusion, FusionCatcher
    4.2 Filtering and report using in-house script
    4.3 Fusion images using Arriba
  5. Exon skipping using in-house script and ctat-splicing
  6. ID-SNP calling using bcftools
  7. QC
    7.1 QC measures from Samtools, Picard, FastQC, Mosdepth
    7.2 MultiQC hmtl report
    7.3 House keeping gene coverage
    7.4 Sample mixup check