Percentage of samples covered per region in IGV

Question

[monica]

Hello everyone,

I was able to generate a .tdf file with multiple bam files for the coverage using an igv tool "count". It only displays the number of reads covered in a particular region. I also want another track to show how many samples were covered by region. How can I achieve this in IGV.

Thank you so much in advance.

[cmdcolin]

it may help to clarify what you mean by "samples". you mean aggregating read counts at each position across multiple bam files? or aggregating, for each position, how many of that bam files had >1 read at that position?