Dear GATK Team,
We've noticed a CNV being called in some samples, but not being called as significant in others, despite a mean log2 copy ratio of -26, and are unsure why this is happening.
We called variants on unpaired canine cancer cell lines, using a panel of normals from unmatched dogs. For calling, we used the Terra GATK somatic CNV pipeline:
- 1_CNV_Somatic_Panel (v.1.3.1)
- 2_CNV_Somatic_Pair (v.1.3.0)
Our data was fairly noisy with the default settings, so we ended up implementing some smoothing options:
- num_changepoints_penalty_factor 5
- kernel_variance_allele_fraction 0.8
- kernel_variance_copy_ratio 0.8
An example of the CNV being called in one sample but not another:
chrX position1 position2 427 -26.224015 -
chrX position1 position2 427 -26.003399 0
These examples were the same sex, and so were run with the same PoN. Can someone help us to understand why this is happening?
Thank you for your help!