Can I run SVIM with multi threads?

[tjiangHIT]

Hi, SVIM is a good SV caller and can be implemented easily. Could I run it with multithreading and how to do like this? Hope your reply. Thank you!

[eldariont]

Hi, thanks for the good question. At the moment SVIM cannot be run with multiple threads unfortunately. But in my experience, the speed of SVIM was sufficient to process even large datasets in a few hours. I could try to add multithreading support when I have time, though, if it is needed. Do you use SVIM on a very large dataset or why are you asking? Cheers David

[tjiangHIT]

Thank you for your prompt reply. I have some simulated datasets for generation of callset with extremely high coverage. I just want to obtain the VCF file quickly. If SVIM can be used with multiple threads, it will have a more broad application prospects in the future.

[wdecoster]

If the current implementation is too slow you could split your dataset per contig/chromosome and run SVIM on those in parallel, merging the vcfs afterward. In my experience, it is sufficiently fast, but the highest coverage I use is 80x.

[eldariont]

Okay, I agree that this would be a useful feature. I put it on my to-do list but cannot promise anything because of my busy schedule right now. For your experiments, it would indeed be a good idea to split up the dataset as Wouter suggested. Would that be an option for you?

[tjiangHIT]

Thanks for the suggestion and I'll try it as soon as possible. Best Tao

[jdmontenegro]

Hi guys, any updates on this? I am trying to use SVIM on a large plant heterozygous genome and I expect to find thousands of heterozygous structural variants compared to the current reference. Some of the SVs could be interchromosomal translocations, so it would be better to keep the entire genome together for this run. Any suggestions?

Best regards,

Juan D. Montenegro

[eldariont]

Hi Juan,

first of all, sorry for my late reply and thanks for your question. Unfortunately, there are no real updates on this except that multi-threading is still on my to-do list. I totally see that this feature would be helpful for your analysis but as I'm in the middle of writing my thesis I cannot really promise anything. I will reopen this issue and try to implement multi-threading as soon as I can.

Cheers David

[jyw-atgithub]

Hi @eldariont , Are you still considering adding the multi-threading feature? Thanks!