Open SimonaSecomandi opened 2 years ago
It's tough to say what's going on from here. You can check to make sure you pack file has coverage using vg depth -k
. Otherwise if you are able to share your input I can take a look.
vg call
has been running too slow on some graphs coming out of cactus and pggb. This can happen in the presence of really large sites. One simple thing that would speed it up would be an option to just bypass such sites (and only call nested variations inside them).
Glenn, I agree that skipping the big sites is a good idea. Alternatively you might want to only genotype the big sites. Maybe a size range limit parameter would support that?
On Thu, Nov 4, 2021, 15:16 Glenn Hickey @.***> wrote:
It's tough to say what's going on from here. You can check to make sure you pack file has coverage using vg depth -k. Otherwise if you are able to share your input I can take a look.
vg call has been running too slow on some graphs coming out of cactus and pggb. This can happen in the presence of really large sites. One simple thing that would speed it up would be an option to just bypass such sites (and only call nested variations inside them).
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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 going, but the VCF is still empty
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 specified size range
I'm interested in calling SNPs, so what size sould I set?
Many thanks!
Maybe something like -C 100
? That should run through rather quickly at least.
Perfect, thank you! I will try it right away and I get back to you as soon as it finishes!!
1. What were you trying to do?
Call variants from read support.
2. What did you want to happen?
Generate a VCF file.
3. What actually happened?
The command have been running for 5 days but the VCF is empty.
5. What data and command can the vg dev team use to make the problem happen?
I have a pangenome graph constructed with Cactus pangenome pipeline. It contains 10 bird assemblies (around 1 Gbp each) for the same species.
Here's the call command:
vg call -t 32 WGS_aug.xg -k WGS_aug.pack > WGS_calls.vcf
Here's the commands I used before this:
6. What does running
vg version
say?