Problem with Sniffles pipeline and SV calling help

Question

[njornet]

I want to perform SV calling on nanopore data. From the resulting bam file after aligning and sorting I add the MD flag with samtools calmd and then run sniffles

sniffles -m alignment_md.bam -v SV_calls.vcf

Then when I want to sort the .vcf I get

FILTER 'STRANDBIAS' is not defined in the header

From what I've seen, the VCF is missing a FILTER option but I can't find how to choose the configuration for the missing filter. Anyway, I added it from someone asking another thing that happened to include this filter in their file:

##FILTER=<ID=STRANDBIAS,Description="VariantStrandBias < 0.02 && StrandBias > 0.02">

After doing that I'm able to sort the .vcf but I don't know how to interpret this. Is the a way to compare the called SVs with a database to see which of them are annotated similar to doing so with ClinVar for SNVs? Or should I just check if the called SVs correspond to the ones causing the diseases in my study?

[GenoMax]

From the resulting bam file after aligning and sorting

How was this done? MD tags should only be required if you did not align to a reference. Aligning with minimap2 followed by sorting should allow you to run sniffles on the sorted BAM.

Answer 1

[Pierre Lindenbaum]

After doing that I'm able to sort the .vcf but I don't know how to interpret this.

what is 'this' ? the broken VCF ? a description of the FILTER was missing in the header (bad workflow, programming error, etc...)

Is the a way to compare the called SVs with a database to see which of them are annotated similar to doing so with ClinVar for SNVs?

you could start with https://lbgi.fr/AnnotSV/