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qbic-pipelines/vcftomaf: 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:

  • BCFtools - Utilities for variant calling and manipulating VCFs and BCFs
  • LiftOver VCF - Lifts over a VCF file from one reference build to another
  • vcf2maf - Conversion of vcf to maf format
  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution

Bcftools

Output files
  • bcftools/
    • *.vcf.gz: PASS and optionally target bed filtered and compressed VCF file.

BCFtools is a set of command-line tools for variant calling and manipulation of Variant Call Format (VCF) files and their binary counterpart BCF.

LiftOverVCF

Output files
  • liftover/lifted
    • *.vcf.gz: liftover VCF file.
  • liftover/unlifted
    • *.vcf.gz: Variants that could not be lifted over
  • liftover/logs
    • *.liftover.log: Logs with liftover statistics

Picard LiftOverVCF is a tool for "lifting over" a VCF from one genome build to another, producing a properly headered, sorted and indexed VCF in one go.

VCF2MAF

Output files
  • maf/
    • *.maf: Contains converted VCF files in Mutation Annotation Format (MAF).

vcf2maf is a perl script to convert VCF to MAF format.

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.
    • Parameters used by the pipeline run: params.json.

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.