BreakDancer and SVDetect do not use read depth to call copy number changes. They use discordant read pairs to detect breakpoints and call structural variants (SVs) from that.
BreakDancer and SVDetect are also quite old and there are better programs using more sophisticated algorithms that have much better performance. I strongly recommend you do not use BreakDancer. It is designed from 2x36bp reads and is outperformed by every SV tool I have compared it against (10+) on data from current sequencers (e.g. 2x100bp). Longer read lengths actually make breakdancer's performance worse! My benchmarking of SV detection in Illumina short read sequence data leads me to recommend GRIDSS^ or manta. Both GRIDSS and manta report variants using the VCF file format.
If you want to call copy number changes, you should use a copy number caller. There are many of these available include sequenza, ABSOLUTE, absCN-seq, FACETS, and many others.
^ Disclaimer: I am the author GRIDSS.
modified 5 weeks ago
5 weeks ago by
d-cameron • 1.0k