A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi. Is there any pipeline using strelka2 for variant calling in rnaseq? There is gatk pipeline, but it takes long.

we have haplotypecaller in <#C01NHS4CC91>

I assume running strelka2 would need a similar logic, right?

Yes, but strelka was archived. Any idea using it would impact the results?

Ok. Is it used in rnaseq? Sarek is wgs based

not in rnaseq, rnaseq does mainly preprocessing, downstream anaylysis is done in <#C045UNCS5R9> or in <#C01NHS4CC91> for example

I mean if you have bam/cram files, you should be able to run sarek on it via the step variant_calling, so there would not be any pre-processing