Summarization

Report pipeline

Once all of your processing pipelines have completed (conventional DNA-Seq for variant calling, sWGS for tumour fraction estimation and EM-Seq for methylation evaluation), you can combine the results into cohort-level and patient-level outputs.

Generate the cohort-level and patient-level summary files and reports (only run this after each of the above pipelines are complete!):

perl ~/git/MismatchResolveDx/scripts/report/make_multimmr_reports.pl \
-w /path/to/swgs_pipeline_config.yaml \
-d /path/to/dna_pipeline_config.yaml \
-e /path/to/em_pipeline_config.yaml \
--output_directory /path/to/output/Patient_Reports \
-c slurm \
--dry-run { optional }

This will use the output directories specified in each config file to find the individual output files from each pipeline.

• From sWGS, this will pull in the QC files and ichorCNA tumour fraction estimates
• From DNASeq, this will pull in the QC files, mutation calls (germline and somatic SNV/INDELs and somatic CNAs) and MSI estimates
• From EMSeq, this will pull in the QC files and methylation estimates

Directory Structure

Patient_Reports
├── Methylation
├── Mutations
├── QC
├── Reports
│   ├── PATIENT1
│   └── PATIENT2
├── SUMMARY
├── data
│   ├── DNASeq
│   │   ├── CNAs
│   │   ├── Contamination
│   │   ├── Coverage
│   │   ├── ENSEMBLE
│   │   ├── Germline
│   │   ├── MSI
│   │   ├── Mutect2
│   │   ├── Pindel
│   │   ├── SVs
│   │   ├── SomaticSniper
│   │   └── VarDict
│   ├── EMSeq
│   │   ├── Methylation
│   │   └── QC
│   └── sWGS
│       ├── CNAs
│       └── QC
└── logs

Methylation: contains cohort-level methylation levels (sample x MMR genes)

Mutations: contains cohort-level mutation data (germline and somatic (ENSEMBLE) mutations for MMR genes)

QC: contains cohort-level QC plots

Reports: contains patient-level reports

SUMMARY: contains cohort-level panel summaries