Introduction Usage Parameters 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:

When —skip_demultiplexing false (default behavior)

LIMA

Output files
  • lima/
    • <sample><barcode-pair>.bam: The demultiplexed bamfiles
    • <basename>.bam.pbi: The Pacbio index of bam files
    • <sample>.lima.counts: Counts of the number of reads found for each demultiplexed sample
    • <sample>.lima.report: Tab-separated file about each ZMW, unfiltered
    • <sample>.lima.summary: File that shows how many ZMWs have been filtered, how ZMWs many are same/different

LIMA demultiplex samples

Note:

  • If —skip_demultiplexing true <basename> = <sample>
  • If —skip_demultiplexing false <basename> = <sample>.<barcode-pair>

PBMM2

Output files
  • pbmm2/
    • <basename>.aligned.bam: Aligned BAM

PBMM2 Aligned BAM files

SAMTOOLS

Output files
  • samtools/
    • <basename>.sorted.bam: The sorted BAM file.
    • <basename>.sorted.bam.bai: The indexed BAM file.

SAMTOOLS Sort and index aligned bams.

GATK4

Output files
  • gatk4/
    • <basename>.vcf.gz: VCF of the SNV
    • <basename>.vcf.gz.tbi: Associated indexes for the VCF files

GATK4 HaplotypeCaller - SNV detection and Variant Call tool.

PBSV

Output files
  • pbsv/
    • <basename>.pbsv.vcf: VCF of SV
    • <basename>.svsig.gz: File containing signatures of structural variants

PBSV. Discover and call structural variants

HIPHASE

Output files
  • hiphase/
    • <basename>.phased.bam: Haplotagged BAM
    • <basename>.phased.vcf: The phased Variant File
    • <basename>.phased.vcf: This CSV/TSV file contains information about the the phase blocks that were output by HiPhase.

HIPHASE

TABIX

Output files
  • tabix/
    • <basename>.vcf.gz: Zipped PBSV VCF files

TABIX VCF file handler - VCF zipping.

BCFTOOLS

Output files
  • BCFTOOLS/
    • <basename>.vcf.gz.csi: Index of PBSV VCF files

BCFTOOLS Manipulates VCF files including Indexes them

DEEPVARIANT

Output files
  • deepvariant/
    • <basename>.vcf.gz: Zipped VCF file
    • <basename>.vcf.gz.tbi: Associated index to zipped VCF file

DEEPVARIANT SNV caller

TRGT

Output files
  • trgt/
    • <basename>.bam.vcf.gz: VCF file for the repeat region
    • <basename>.bam.spanning.bam: BAM for the repeat region
    • <basename>.svg: Waterfall plot of the repeat region

TRGT Plots and Genotypes tandem repeats

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.