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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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Sniffles failing to detect 5bp deletion? #330

Closed caonetto closed 2 years ago

caonetto commented 2 years ago

Hi, I am currently testing sniffles in samples that have been genetically modified with a 5bp deletion. I am currently running the following parameter without filtering any QC sniffles --input ref.s.bam --minsvlen 3 --vcf ref.vcf --snf ref.snf --threads 50 --allow-overwrite --minsupport 10 --reference ref.fasta --qc-output-all

Is there a minimum size for SVs that is supported by sniffles?

Cheers. sniffles_screenshot

fritzsedlazeck commented 2 years ago

Dear @caonetto Sniffles2 is not recommended for small indel calling. I think we tested it down to 10bp but certainly not below. I would recommend e.g. Clair v3 for these things. Thanks Fritz

caonetto commented 2 years ago

No worries Fritz,

Thanks for your quick response.

Cheers.