Structural variants calling in a population

Question

[guillaume.rbt]

Hi all,

I'm currently struggling with structural variant calling.

I would like to call those structural variants for all samples in my population of haploid fungi (around 100).

My aim is to cross the results of all samples to get absence/presence polymorphisms of all called variants.

Would anyone know a tool that is able to call variants on all samples, and then cross the results to have only one file with SVs presence/absence for all samples?

Thanks in advance for your help

Guillaume

EDIT : I've eventually been using Delly2, which can handle multi-sample calling

Answer 1

[Rohit]

If you are planning to look for Indels mainly, then Freebayes performs well for population data. But if you also interested in other SVs too, then you would need one of the SV-caller pipelines seperately on each of the populations and then look for those which are common in all, since calling it in one go for all populations would just go to majority voting through read-support - not sure if any of these are population based though

Answer 2

[Benbird]

There are multiple tools for individual sample SV calling. SV-Pop could help to postprocessing individual calling results and merge them as population-level files. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2718-4