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.