Skip to content
Investigate coverage metrics for variant calling experiments
Clojure
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
config
src
test
.gitignore
README.md
project.clj

README.md

bcbio.coverage

Summarize coverage of high throughput sequencing experiments, emphasizing approaches that identify poorly covered genes or pathways of biological interest. Current variant calling and prioritization approaches identify potentially deleterious mutations, but do not provide an easy way to summarize regions with low or no coverage where we may have missed variants due to coverage issues.

The inputs are:

  • BigWig file of coverage or BAM file from which we can calculate coverage.
  • BED file or list of gene identifiers of genes of interest.

and it outputs:

  • Ranked list of gene regions with low or no coverage, prioritized by: coding region coverage and total bases missed.

Longer term goals include handling non-coding region prioritization.

Resources

License

The code is freely available under the MIT license.

You can’t perform that action at this time.