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Multi-sample coverage browser

Project description

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.

significant_regions

Proportions covered

proportional_coverage

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 [bpedersen@base2genomics.com].

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