Chanjo - Coverage analysis for clinical sequencing

Intro

$ cat intervals.bed | chanjo annotate alignment.bam
#{"sample_id": "bavewira", ...}
1	10	15	interval-1	9.922	0.97231
2	45	55	interval-2	14.231	1.0

Chanjo adds two columns to each genomic interval (e.g. exon) describing average coverage and how many percent of bases that are covered at 10x reads; completeness.

To learn more about Chanjo and how you can use it to gain a better understanding of sequencing coverage you should start by checking out the demo.

Overview

Chanjo works on BAM alignment files and extracts interesting coverage related statistics. You use a BED-file to define which regions of the genome that you particularly care about. The output takes the shape of an extended BED-file.

An optional final step is to load results into a SQL database. This will aggregate data from exons to transcripts and genes. The database later work as an API to downstream tools like the Chanjo Report generator.

Documentation

The comprehensive documentation has all the information you want; getting started guide, foolproof installation instructions, and in-depth overviews.

Installation

Complete instructions are available in the docs but if you know what you are doing, Chanjo is installed by simply running:

$ pip install chanjo

Contributors

Robin Andeer (robinandeer, robinandeer)

Luca Beltrame (lbeltrame)

John Kern (kern3020)

License

MIT