Detecting aneuploidy in sequencing data or copy number profile?

Question

[vctrm67]

Is there a package/way to detect per-chromosome aneuploidy for NGS data or copy number profiles?

[Pierre Lindenbaum]

get the average depth for the whole genome and compare with the depth per chromosome ?

[vctrm67]

But let's say I had a whole genome duplication and then one of the chromosomes was subsequently deleted (so 4 copies of each chromosome). By read depth only, everything would still have the same read depth except that one chromosome. Wouldn't it be difficult to distinguish this case from simply aneuploidy of the chromosome without a whole genome duplication because the relative read counts in either case would be the same?

[vctrm67]

Also for whole genome duplication.

Answer 1

[igor]

A lot of the copy number packages will use BAFs to try to estimate ploidy. The Sequenza paper has a nice figure illustrating how this is possible: