Is it possible to compute the Loss of heterocigosity from the Copy number variation (CNV) data file ?

Question

[aliciapm94]

I need to compute the LOH and LST. Is it possible to compute it directly from the CNV data ?

[Pierre Lindenbaum]

how can we know the nature of "the CSV data" ?

[aliciapm94]

Sorry, I meant copy number variation

Answer 1

[d-cameron]

If the copy number does allele-specific copy number calling then yes, a LOH region is simply a region with minor allele copy number of zero.

Whether it can be done on your data depends entirely on what copy number caller was run as they all have different output formats.

[aliciapm94]

Thanks a lot for the answer, would it be possible to compute also the large scale transitions LSTs?