Extracting haplotype-specific annotations from splicing graph

Question

[Juhyun]

Hi developer,

I have a quick and very ambiguous question regarding transcriptome graph analysis. Is there any way to extract or retrieve the projected(liftover) transcriptome annotation in a graph from reference annotation to each haplotype, formatted in GTF or another format based on haplotype coordinates?

My graph was generated using the command below:

vg rna -p --threads $SLURM_CPUS_PER_TASK \ 
                    -q \ 
                    --transcripts ${wd}/03.pantranscriptome/${chr}.gtf --gbz-format \ 
                    --write-gbwt ${wd}/03.pantranscriptome/${chr}.pantranscriptome.gbwt \ 
                    --write-info ${wd}/03.pantranscriptome/${chr}.pantranscriptome.txt \ 
                    -f ${wd}/03.pantranscriptome/${chr}.pantranscriptome.fa \ 
                    ${wd}/02.minigraph-cactus/${prefix}.${chr}.gbz \ 
                    > ${wd}/03.pantranscriptome/${chr}.spliced_graph.pg

The "--proj-embed-paths" parameter inspired me this idea. If you have any possible way to do that, please let me know. \ it would be very helpful to me! : )

Thanks,\ Jh

[Jordan M Eizenga]

In principle, it wouldn't be hard to do that, but this feature is not currently implemented in vg. You could consider opening a feature request on the vg GitHub page if this is something that would be important for your research.