Hi everyone, is this pipeline suitable for benchmarking of variant callers that detects somatic structural variants SVs in tumor samples? I saw in the docs that the pipeline does not include a tool specifically dedicated to somatic SV benchmarking, so I’d like to confirm whether it’s appropriate for this use case, thanks

Hello, yes you can use it for somatic SV benchmarking (even-though it does not have a somatic SV specific benchmarking tool - which does not exist). please check this example https://github.com/nf-core/variantbenchmarking/blob/dev/conf/tests/somatic_sv.config.

Ok, thank you! Do I need to use dev branch or master is already ready to use?

You can use latest release 🙂 Dev should also work..

and one more question - when I am going to use my own truth dataset, validated somatic variants respectively, is there specific procedure how to create the vcf or it should just follow the same format as my sample vcfs?

a valid vcf, with GT, SVLEN and SVTYPE should work. For complex variants, truvari handles, yet wittyer and svbenchmark might cause some issues. Please let me know if you encounter any issues 🙂