search

fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
Other
546 stars 91 forks source link

[Question] Recommended visualization method for multi-sample VCF #394

Open jolespin opened 1 year ago

jolespin commented 1 year ago

I have just successfully run Sniffles2 with ~45 yeast genomes. What is the recommended way to visualize multi-sample VCF files generated from Sniffles?

fritzsedlazeck commented 1 year ago

Sadly there are not really any solutions for this. did you do the merging also in Sniffles?

SURVIVOR has some packages to help you QC the overall stats. In general its a VCF file so its a common problem to generate plots with small coding required. There are some examples online but nothing like a finished thing. You should be able to use this VCF as any other SV VCF. Sorry Fritz

jolespin commented 1 year ago

Oh ok no worries. Thanks for creating this tool btw. The only one that is well documented, easy to install, and works well 🙏🏾.

Is SURVIVAL the package you would recommend for calculating stats in insertions, deletions, translocations, etc?

fritzsedlazeck commented 1 year ago

Thanks, we have now just implemented a small python package to plot and help with QC of Sniffles output. Please try this and give feedback: https://github.com/farhangus/sniffles2_helper