covviz 1.0.3

Multi-sample coverage browser

covviz

Coverage visualization; a companion viewer for indexcov results.

Here we use indexcov to quickly estimate the coverage across samples then find regions of large, coverage-based anomalies. The aim is to highlight regions of significant (passing the user's z-score threshold) and sustained (beyond user specified distance) deviation from the majority of samples. Significance is determined using z-scores (--zthreshold) for all samples at all points using median absolute deviation, but in order to be highlighted, points must be significant consecutively throughout a user specified distance (--distancethreshold).

Usage

Install nextflow:

curl -s https://get.nextflow.io | bash

Full nextflow installation instructions are available at: https://www.nextflow.io/

To simplify prerequisite software installations and software version tracking, we strongly recommend running covviz using Docker or Singularity. Docker installation instructions for your operating system are available at: https://docs.docker.com/install/

Then, with Docker or Singularity we run:

nextflow run brwnj/covviz -latest -profile docker \
    --indexes 'data/indexes/*.crai' \
    --fai data/g1k_v37_decoy.fa.fai \
    --gff data/Homo_sapiens.GRCh37.82.gff3.gz

Which gives us ./results/covviz_report.html.

Required arguments

• --indexes
  • quoted file path with wildcard ('*.crai') to cram or bam indexes
• --fai
  • file path to .fai reference index
• --gff
  • file path to gff matching genome build of --indexes

Options

• --outdir
  • output directory for results
  • default: "./results"
• --sexchroms
  • sex chromosomes as they are in --indexes
  • default: "X,Y"
• --exclude
  • regular expression of chromosomes to skip
  • default: "^GL|^hs|^chrEBV$|M$|MT$|^NC|random$|Un|^HLA\-|_alt$|hap\d+$"
• --zthreshold
  • a sample must greater than this many standard deviations in order to be found significant
  • default: 3.5
• --distancethreshold
  • consecutive significant points must span this distance in order to pass this filter
  • default: 150000
• --slop
  • leading and trailing segments added to significant regions to make them more visible
  • default: 500000
• --project
  • can be used to name your indexcov to something more meaningful
  • default: "NF"

Report

Interactive example

See: https://brwnj.github.io/covviz/

Scaled chromosome coverage

Significant regions will be displayed in color atop a gray region which represents the upper and lower bounds of a given point minus any values deemed significant.

Proportions covered

The metadata table will be displayed below the plots.

Interaction

Clicking on plot traces highlights the line and searches the metadata. Double-clicking de-selects lines, resets the plot, and de-selects samples from the table. Clicking on the gene track launches a search for the gene's respective Gene Card. In cases where genes overlap, multiple windows/tabs will be opened.

License

covviz is free and unrestricted for non-commercial use. For commercial use, please contact [[e-mail]].