Common parameters still relevant in multi-sample mode

[eliavw]

Hi,

From the --help page I've deduced that Sniffles categorizes its parameters in a few categories

• Common parameters
• SV Filtering parameters
• SV Clustering parameters
• Multi-Sample Calling / Combine parameters
• SV Postprocessing, QC and output parameters

Based on this, one would expect that in multi-sample mode, the following categories are relevant

• Common parameters
• Multi-Sample Calling / Combine parameters
• SV Postprocessing, QC and output parameters

That being said, I was wondering about some parameters in the first category, specifically:

• reference
• tandem-repeats
• non-germline
• phase

all of these are obviously relevant when calling variants, but to which extent do they still matter in multi-sample mode? It is my understanding that multi-sample mode focuses on combining already called SVs present in the individual snf files provided as inputs. It is unclear to me how e.g. a reference sequence would still matter in that case.

Thanks!

[fritzsedlazeck]

Hi, I am not sure I am following. There is a section "Multi-Sample Calling / Combine parameters:" which lists the merging relevant parameters. The parameters are otherwise categorized for different steps in the program.

Thanks

[eliavw]

Hi,

Sorry for the confusion.

I understand that there is a section for parameters related to multi-sample calling, that is clear.

My question is about the "common parameters". Some of those evidently still apply in multi-sample mode (e.g. -i to specify inputs, -v to specify vcf file etc), whereas others like (--reference) seem only relevant when using Sniffles to call SVs in a single-sample.

Is that understanding correct?

Thank you!

[eliavw]

Maybe an example to make it more concrete;

sniffles --input sample1.snf sample2.snf ... sampleN.snf --vcf multisample.vcf --reference some_genome.fasta

In the command above, I would assume that specifying a reference (--reference some_genome.fasta) is irrelevant since the .snf files already contain called variants from prior (single-sample) runs of sniffles.