SimonaSecomandi
SimonaSecomandi
Many thanks for you answer!! I managed to generate the augmented graph on a 1 TB RAM node!
Thank you for your support! I generated the index with those commands: ``` vg prune -t 32 -k 45 pangenome.vg >pangenome_pruned.vg vg mod -t 32 -X 256 pangenome_pruned.vg > pangenome_pruned_mod.vg...
Hello, I managed to index, prune and align my illumina WGS data against the variation graph. ``` vg mod -t 32 -X 256 .pangenome.vg > pangenome_chopped.vg vg index -t 32...
Dear all, I can't share my graph, the augmented vg praph is 80 Gbytes.. I'm checking the coverage with `vg depth -k WGS_aug.pack WGS_aug.vg ` Meanwhile, the calling is still...
Hi all, I saw that you implemented an option to avoid calling large snarls (#3490): `Options -c and -C added to vg call to restrict snarl calling to sites within...
Perfect, thank you! I will try it right away and I get back to you as soon as it finishes!!
Hi @adamnovak , many thanks for the support! The strange SNPs were fixed by` vg mod -O` (see before and after images)!! Do you think this is the best way...
Update: I re ran the commands with vg giraffe just to check if the problem was the vg frozen version used for vg safari: ``` $vg giraffe -t $cpus -p...
Hi Adam, I am sorry for the late reply. I'll replicate the error and extract the "problematic" reads early next week. Meanwhile, how could I share the graph and the...
Hi Adam, unfortunately there is no such information in the crash file (like which reads caused the crash). I already have the `-p` flag in vg giraffe/safari. I am also...