Hi Tobias,
I saw here that delly lr now supports a sort-of pangenome-aware mode where you still call variants with respect to a linear reference but you can exclude those that are also present on a different linear reference and on a pangenome graph, which is super cool.
I was wondering - would it be possible to have this available in delly call as well? I don't see the -l flag exposed in the call sub-command. Maybe there is a technical reason this is currently not possible with short-reads?
I have reads aligned to the minigraph graph with minigraph --vc -cx sr pangenome.gfa.gz sample.fq.gz.
Best,
Davide
Hi Tobias,
I saw here that
delly lrnow supports a sort-of pangenome-aware mode where you still call variants with respect to a linear reference but you can exclude those that are also present on a different linear reference and on a pangenome graph, which is super cool.I was wondering - would it be possible to have this available in
delly callas well? I don't see the-lflag exposed in thecallsub-command. Maybe there is a technical reason this is currently not possible with short-reads?I have reads aligned to the minigraph graph with
minigraph --vc -cx sr pangenome.gfa.gz sample.fq.gz.Best,
Davide