Closed daisyyr closed 2 months ago
Hi,
thank you for using Battenberg and for reporting this issue. Would it be possible to see the plots with the LogR and BAF for this execution: <tumour_label>.tumour.png
(and <tumour_label>.germline.png
if available)?
Hi ~ I'm using Battenberg on my tumor WGS data and have encountered some issues with certain samples. For example, in the sample.BattenbergProfile_average.png (A) and sample_copynumberprofile.png (B) shown below, the total copy number of some chromosomes (e.g., chr3, chr4, chr5) appears to be 0. However, when I used GATK4 to call segmental CNVs, the total copy number of these chromosomes (e.g., chr3, chr4, chr5) was equal to 2 (C).
What might be causing these discrepancies? Many thanks in advance for your help. I look forward to your reply. Here is the code I used.