Introduction

This document describes the output produced by the pipeline. Many workflow summaries are visualised in the MultiQC report generated at the end of the run.

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

Coordinate file indexing

Coordinate-based output files (text formats) are automatically compressed with bgzip and indexed using tabix. Each such file is accompanied by three index files:

  • .gzi: GZ index (for internal gzip block lookup)
  • .tbi: Tabix index (standard block-gzip index)
  • .csi: Coordinate sort index (for large files or CSI-based applications)

All listings below refer to the main file only; indexes are generated automatically alongside it.

Pipeline overview

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

  • VCF index - Create index of input variant files
  • VCF processing - Process files to analyse SNP density, InDel sizes, per-base nucleotide diversity, heterozygosity, and allele frequency
  • ROH analysis - Detect and visualise runs of homozygosity, including multi-sample split outputs
  • VCF stats - Parse input files, produce text stats, and generate plots
  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution

VCF index

The pipeline first looks for existing TBI or CSI index next to the input variant file (same name, with an extra .tbi or .csi). If there isn't, use tabix to generate index files for input variants.

Output files
  • Tabix index: <sample_input_file>.tbi
  • CSI index: <sample_input_file>.csi

Depending on sequence length and input type, one or both index types may be produced.

VCF processing

Output files
  • Single nucleotide polymorphisms (SNP) density: <filename>.snpden.gz (indexed).
  • Insertion or deletion (InDel) sizes histogram: <filename>.indel.hist.
  • Per-site (per-base) nucleotide diversity: <filename>.pi.gz (indexed).
  • Heterozygosity: <filename>.het.
  • Allele frequency: <filename>.frq.gz (indexed).

ROH analysis

Output files
  • Interactive ROH visualisation: <filename>.roh-viz.html.
  • RG (region group) subset of ROH output: <filename>.roh.rg.gz (indexed).
  • ST (site-specific) subset of ROH output: <filename>.roh.st.gz (indexed).

For multi-sample VCF inputs, RG and ST outputs are split per sample, with sample-specific filenames <filename>.<sample-name>.roh.* (sample names from the VCF file itself).

VCF stats

Output files
  • Summary statistics generated by BCFtools (output compressed): <filename>.bcftools_stats.txt.gz.
  • PDF plots generated by plot_vcfstats: <filename>.plot-vcfstats.*.pdf.

MultiQC

Output files
  • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.

MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project.

Results generated by MultiQC collate pipeline QC from the tools used in this workflow. 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.