Skip to content

Latest commit

 

History

History
58 lines (48 loc) · 1.75 KB

README.md

File metadata and controls

58 lines (48 loc) · 1.75 KB

README

Circos is a popular tool for visualizing genomic data. The contained scripts provide data files and configurations for circos plots that combine raw read counts, copy number calls and translocations.

Usage

calls BED

To convert a *_calls.bed generated from the wf-cnv pipeline from ONT to usable copy number call track:

python convert_bed_to_cnv_track.py --sample <sample name> --bed <full path to bed file> --type calls

This will generate the following output file:

<sample>.calls.fixed.bed

Note that 0 values in the call column will be removed to create a readable circos track.

raw BED

To convert a *_raw_bins.bed file, generated from the wf-cnv pipeline from ONT, to a binned read depth track:

python convert_bed_to_cnv_track.py --sample <sample name> --bed <full path to bed file> --type raw

This will generate the following output file:

<sample>.raw.fixed.bed

translocation LINK

LINK tracks in circos require a similar file format to BEDPE. However, an additional meta data column provides a colour to differentiate inter-chromosomal (black_a5) and intra-chromosomal (red_a5) link lines in the circos plot:

python convert_bedpe_to_link.py --sample <sample name> --bedpe <full path to the translocation BEDPE file>

This will generate the following output file:

<sample>.translocation.fixed.link

Snakemake

A snakemake pipeline has been created to simplify the process:

snakemake --configfile <YAML config file> -s Snakefile --cores <number of cores> all

This will produce all three files and can be expanded to execute circos.

circos.example.conf

An example circos configuration file is provided in circos.example.conf. Note that the file parameters will need to be changed.