Full chromosome aneuploidy detection

Question

[VHahaut]

Hello!

I am looking for a software that could detect automatically full chromosome aneuploidy from whole-genome sequencing data (cancer vs germline). Those deletions/duplications are fairly obvious by eye but we would like to confirm them with a second more automatized method. I found plenty of tools to find small/large rearrangments but nothing so far can pinpoint all chromosome modifications. The reference genome is well annotated but still contains plenty of gaps.

Could you tell me what is the best tool for this job?

Answer 1

[Wayne]

You may want to look into Brent Pedersen's indexcov for visualization, see here, here, and here.

As I discussed here, I made a Python script called plot_expression_across_chromosomes.py that may work if you have components that should produce a one to one ratio when normally in euploid state. In response to your question and in light of Pfundt et al 2016, entitled "Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders" where they talked about screening 2,603 sample, I added the option for a really simple assessment to give user an automated heads up when aneuploidy may be indicated at the chromosome or scaffold level. It requires running the script with the --smooth option.

Also you may want to see here and here