sciClone input LOH

Question

[shumaila.sayyab]

Dear all,

I want to use sciclone on my somatic variant data. I am confused about the input it takes. One is the CNA information but incase of LOH input file, Is it cnLOH or LOH ? what i mean is looking at the results from ASCAT, should i give regions where we have major 2n and monir 0, or all the regions where the minor is 0 with major allele could be 2n, 3n trisomies, so on etc...

Can anyone explain what LOH files mean here in context of sciclone input?

Thanks in advance.

[shumaila.sayyab]

perhaps, this may be the answer to what i was looking.. which i missed earlier The meaning of VAF and LOH in sciclone

[Chris Miller]

Yep, that's the definition you're looking for. Hope it cleared things up!