Question regarding columns in regions.bed and cnv.bed outputs

[TrentPrall]

Hi there,

I am a new user so far I've been really impressed with your tool, so thank you. I have a question regarding what the columns in the regions.bed and cnv.bed outputs are reporting. Particularly the last columns in each bed file. I believe the depth is reported in the final column of cnv.bed, and that this depth represents the factor of read depth against the expected, normalized read depth for the reference genome. Is this correct? In regions.bed, is the final column the expected read depth within each bin? Any clarification would be helpful.

Thank you.

[philippesanio]

Hi @TrentPrall

Thank you!

The regions.bed.gz file originates from Mosdepth, and the last column represents the read depth per bin (e.g. 1kb). The last column in the output file cnv.bed.gz from Spectre is the ploidy normalized coverage within the CNV start and end position. It can also be used to indicate the copy number (CN). E.g. if the value in the last column is ~3 then the CNV would be a DUP with CN 3 (assuming ploidy 2 for the sample)

If you have any further questions, please reach out any time! Best, Philippe