I'm using IGV to display CNV data, and for some tracks there are no CNVs.. but for some reason IGV renders these 'empty' tracks in blue..
Any suggestions on how to force IGV to color these in White?
Please show a screenshot and give some details on what file format you loaded into CNV.
How to add images to a Biostars post
Here is the image..
Are these segmented copy number files? How did you determine that there are no CNVs on the tracks with blue bars. The blue bar indicates a CN < 2.
Yes, these are segmented CNVs detected using QDNAseq, I know there are no CNVs on the blue tracks by looking at the raw SEG files