Hi @davidebolo1993!
I've found a limitation in VISOR simulations regarding a common structural event: independent chromosomal gains or gains of large chromosomal segments. For example, in Multiple Myeloma it's common to observe +1q gain or whole chromosome 3 gain as free copies, not tandem duplications.
@tdido and I are evaluating SV calling and CNV tools and need to simulate these events. The only workaround I can think of with current options is not very accurate: copy-pasting the chromosome/fragment at the end of another chromosome...
Is there another way to do this with existing options?
Could VISOR include the option to generate total or partial chromosomal duplications as "free" independent copies?
This would be very useful for benchmarking CNV/SV callers in cancer genomics.
Thank you in advance!
Hi @davidebolo1993!
I've found a limitation in VISOR simulations regarding a common structural event: independent chromosomal gains or gains of large chromosomal segments. For example, in Multiple Myeloma it's common to observe +1q gain or whole chromosome 3 gain as free copies, not tandem duplications.
@tdido and I are evaluating SV calling and CNV tools and need to simulate these events. The only workaround I can think of with current options is not very accurate: copy-pasting the chromosome/fragment at the end of another chromosome...
Is there another way to do this with existing options?
Could VISOR include the option to generate total or partial chromosomal duplications as "free" independent copies?
This would be very useful for benchmarking CNV/SV callers in cancer genomics.
Thank you in advance!