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nf-platypusindelcalling: Output

Introduction

This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

  • Platypus - Tool used to call variants. It can detect SNPs, MNPs, short indels, replacements, deletions up to several kb.
  • Annotation - Several databases like gnomAD, dbSNP, mirBASE, COSMIC and ExAC as well as the sequencing regions like selfchains, enhangers, repeat regions or mappability beds are used to create annotations to the variants. Annovar tool is used to annotate and make classifications.
  • Filtering - Filtering can be applied to the annotated files for no-control samples. Extracted indels can be viewed by screenshots.
  • Check Sample Swap - Canopy Based Clustering and Bias Filter, thi step can only be applied into the tumor samples with control.
  • Pipeline information - Report metrics generated during the workflow execution
  • [MultiQC] (#multiqc) - logs, reports and tool versions summarized using MultiQC tool.

Platypus

Output files
  • metaid/
    • indel_metaid.raw.vcf.gz: Platypus called vcf file.
    • indel_metaid.vcf.gz.linesCorrupt : Reports the corrupted lines if exist.
    • indel_metaid.log: Log of platypus

Annotation

Output files
  • metaid/
    • indel_metaid.vcf.gz: Annotated vcf file

Filtration

Output files
  • metaid/
    • indel_metaid_somatic_functional_indels_conf_*_to_10.vcf: Functional somatic indels filtered through the confidence score
    • indel_metaid_somatic_indels_conf_*_to_10.vcf: Somatic indels filtered through the confidence score
    • indel_metaid_somatic_ncRNA_indels_conf_*_to_10.vcf: Somatic ncRNA indels filtered through the confidence score
    • indel_metaid_germline_functional_indels_conf_*_to_10.vcf: Functional germline indels filtered through the confidence score
  • metaid/screenshots/
    • metaid_indel_somatic_funtional_combined.pdf: Screenshots of the variants from indel_metaid_somatic_functional_indels_conf_*_to_10.vcf
    • metaid_indel.json : Indel lenght break down report from indel_HCC1187_somatic_indels_conf_5_to_10.vcf

Check Sample Swap

Output files
  • metaid/
    • indel_metaid.checkSampleSwap_TiN.log: Tinda run log
    • indel_metaid.swap.json: Report of number of compared variants
    • indel_metaid.tinda.vcf : Tinda VCF file
    • snvs_metaid.GTfiltered_gnomAD.Germline.Rare.Rescue.txt : Germline Rare SNVs
    • snvs_HCC1187.GTfiltered_gnomAD.Germline.Rare.Rescue.png : Screenshots of Germline Rare SNVss

MultiQC

Output files
  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.

Pipeline information

Output files
  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter's are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.