Circos karyotype file

Question

[The_PyPanda]

Hi, I'm trying to generate some circos plots for structural variants, using the tool circos. To this I understand I need to specify a karyotype file.

Please correct me if I'm wrong. But my understanding is that I need to create this karyotype file for GRCh38? I currently have my called structural variant data in the following format (bed and csv files).

Chromosome    Start     End
chr1      110000   120000
Chr5     150000   200000

Can I ask is there a tool to convert this data? Or am I going completely wrong and there is a preset Grch38 karyotype file that I need to use?

Thank you in advance

Answer 1

[Pierre Lindenbaum]

https://github.com/node/circos/blob/master/data/karyotype/karyotype.human.hg38.txt

[The_PyPanda]

Thank You Pierre.

[The_PyPanda]

I have one more quick question. Not sure if I should start another thread - apologies if so.

But how do we calculate the value column for Circos. I understand that this is the column Circos reads?

For example: