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