Dear all,
I have a question regarding Copy Number analysis using ABSOLUTE software from Broad Institute.
I want to call CNA for a Tumor with matched Normal and I have both Tumor and Normal bam files.
I have installed ABSOLUTE but I am not sure how to use it for NGS data. I think the example that is given in their website is for array data not for NGS.
thanks much,
--Subhajit
You should not try to use varscan to call CN on WGS. Instead, you should use something like copyCat, or others that support WGS http://omictools.com/somatic-cna-detection-category
Hi Chris, Thanks for your reply. Does copyCat handle WXS data ??
No. VarScan, linked above, is a fine choice for calling copy number from exomes.
Thanks Yunku for your help and Sorry for my late reply.