Overlapping CNVRs

[zainabae]

Hello,

After obtaining the xlsx file of the merged and filtered regions I noticed that several CNVRs were overlapping.

Please Check regions highlighted in yellow

Can anyone please tell me how to solve this issue? And why it happened?

[DLEE-BARC]

Were you able to solve this issue?

[zainabae]

Were you able to solve this issue?

Yes

My mistake was processing each group of samples separately before running the filtering and genotyping step on all of them.

if overlapping regions still appear, Bedtools could be useful.

[DLEE-BARC]

Hi @zainabae,

Thank you so much for the prompt reply!

I am still a little bit confused about the processing steps when multiple samples need to be merged.
Could you please share a little bit more detail on the processing and Bedtools usage? Did you use cnvpytor or cnvnator?

I am just following this '/~https://github.com/abyzovlab/CNVpytor/blob/master/examples/merging.md'.
However, once they were merged, the information gaps with individual files (generated by -call function) occurred.
And lots of overlapping regions.

Please share your wisdom. I appreciate it in advance.