https://github.com/brwnj/covdist
simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.
https://github.com/brwnj/covdist
coverage genomics-visualization
Last synced: 3 months ago
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simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.
- Host: GitHub
- URL: https://github.com/brwnj/covdist
- Owner: brwnj
- License: mit
- Created: 2021-04-27T18:46:53.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2022-05-20T15:58:54.000Z (about 4 years ago)
- Last Synced: 2025-12-13T22:27:32.871Z (6 months ago)
- Topics: coverage, genomics-visualization
- Language: HTML
- Homepage: https://brwnj.github.io/covdist/
- Size: 87.9 KB
- Stars: 4
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# covdist
Perform simple coverage profiling of aligned samples. Admittedly this is
a very simple tool, but is quite useful for sequencing center feedback and
topoffs.
Interactive example: https://brwnj.github.io/covdist/
## Note
This is an extension of mosdepth's plot-dist.py script. See:
https://github.com/brentp/mosdepth/blob/master/scripts/plot-dist.py
Here we run `mosdepth` and generate a very similar report.
# Usage
```
nextflow run brwnj/covdist -revision main -profile docker
--crams '*.cram'
--reference GRCh38.fasta
--gaps GRCh38_gaps.bed
```
## Gap info
A simple way to grab this info, to omit region of known gaps in coverage, is
to head over to:
https://genome.ucsc.edu/cgi-bin/hgTables
1. Under `group:` select `Mapping and Sequencing`.
2. For `track:` select `Gap`
3. Set `output format:` as `BED` and define the file name.
## Autosomes
It is likely important for you to get accurate coverage estimates and to
communicate them with your sequencing center. That said, you likely want
to exclude sex chromosomes using:
```
--exclude "decoy,random,chrUn,alt,phix,chrEBV,chrM,chrX,chrY"
```
# Report
Samples can be subset using the "Samples" filter, which is sorted by ascending median coverage.
You can browse covered on each chromosome or all chromosomes under the label "total".
Target coverage cutoff is set dynamically by the user and updates the table. The table
column is sortable and selections on the table can be made to highlight a given sample.