Tobias Rausch

There are different nomenclatures for head-to-head or 5to5 inversions and so on. Here is a nice [summary figure](https://www.nature.com/articles/s41596-019-0234-7/figures/12). INFO/SR is not exhaustive. Once delly found enough evidence for an SV...

Delly does evaluate split-reads independently so it's indeed surprising that for 150bp reads this SV did not show up. Difficult to tell why without having the data, probably some mis-assembly...

Thanks for sharing the BAMs. I modified the header to include only chr1-22XY because I wasn't aware of an hg19 reference genome with *_fix chromosome names. I get 2 PRECISE...

`read1.fq.gz` and `read2.fq.gz` are the output files of dicey chop. The `srt.bam` file you only need for creating the mappability map: `map.fa.gz`.

For the commonly used reference genome, we do have pre-computed mappability maps [here](https://gear-genomics.embl.de/data/delly/)

Delly realigns reads to the REF and ALT (INFO/CONSENSUS) allele. This does not change the breakpoint position in the VCF file but if reads align equally good to REF and...

Yes, delly computes a consensus to reference alignment using dynamic programming. If you compile from source you can also output this alignment to stderr: [Consensus to reference alignment code](https://github.com/dellytools/delly/blob/main/src/split.h?plain=1#L664-L678)

So the delly VCF is correct or is there a bug in the converter script `delly2bnd.py`?

Hi Darren, Looks like delly's raw CN estimates are in agreement with CNVkit. The assignment of integer copy-number status indeed assumes 100% purity, which is not ideal for cancer genomics...

Yes, please use CN or RDCN. The long answer is: For copy-number variants delly is currently not using the GT field because that's commonly used for hom. ALT (1/1), het....