DNA Copy Number

[arcolombo698]

Hello.

I thank you in advance. I am just interested in finding the DNA copy number from whole DNA sequencing.

note, i am not interested yet in creating SEG files from the circular binary algorithm yet. just need copy number information similar to slide 4 from

http://statweb.stanford.edu/~nzhang/Stat366/lectureHMM.pdf

I am using IGV software, and their website at Broad only mentions the creation of SEG files.

yet , i am aware that from the correct interpretation of IGV one can "eyeball" The DNA copy number.

I am not interested yet in copy number variants, but just the copy number.

I am not sure if the copy number is the same as the count number.

I am not sure if there is software that can calculate the DNA copy number.

From IGV I can not determine the copy number .... here are some images that I am examining, and am just looking for general advice