Provide variants coordinates for all input genomes, not only reference (as in the VCF)

[RRebo]

Hi Cristian,
I was wondering if it is possible to have the polymorphic TE coordinates in all génomes and not only in the ref ? It s quite useful when we map RNAseq and other things to the assemblies and not the ref.

Thanks!
Rita

[clemgoub]

Suggested enhancement: add an output file mapping the VCF (pangenome.vcf) coordinates to each input genome. Probably provide this file in the 3rd output dir 3_TSD_Search/.

Note: it doesn't seem that SVIM-asm raw output provide this information (I only see vcfs in the output folder of the svim-asm processes).