Genome coordinates for PTMs

[ypriverol]

@cschlaffner :

We have an ongoing project to release PTMs and single aminoacid variants coordinate at genome scale. The idea is that the users gave a region of the genome and we can trace all the ptms and variants in that region. Similar to the VCF when every single variant is traced, rather than tracing peptides.

I was wondering if is possible to output in the tool not only the peptide coordinates but also the PTMs coordinates.

[cschlaffner]

@ypriverol :

It is possible to calculate the PTM coordinates and generate BED/GTF output format for those.
VCF format is a bit trickier but I think we could get a workaround going by declaring the PTMs insertions instead of substitutions. In cases where three peptides have 2 PTM sites: (i) one peptide with site 1, (ii) one peptide with site 2, and (iii) one peptide with sites 1 and 2 the resulting output then would be just the two sites individually? Information about cooccurrence would get lost.

[ypriverol]

I think we can put for now, the information of each site without the concurrency.