Sniffles2 doesn't call a large deletion that sniffles1 did call

[paulauitt2]

I tried sniffles2 on some Nanopore data (see picture) with a homozygous RhD deletion. Sniffles1 did call this deletion (min supporting reads 3) and I tried using the exact same parameters on Sniffles2 but for some reason it doesn't call the deletion. Parameters:
sniffles --input input.bam --vcf output.vcf --reference grch38.fasta --minsupport 3.

Someone has any idea on this?

Best wishes,
Paula

[smolkmo]

Hi Paula,

it may be that your variant is being filtered by Sniffles2 due to updated thresholds.

Could you try running your sample through Sniffles2 while adding the --no-qc option? This will make Sniffles2 output also filtered variants. If your variant then shows up, taking a look into its FILTER column value could give a clue as to why it is being filtered.

Best wishes,
Moritz

[paulauitt2]

Hi Moritz,

Thank you very much for your reply. I tried the --no-qc option, but even with this parameter I don't find the deletion back. Good to note, if I use the --no-qc option, the vcf file can not be loaded into IGV..?
I tried to find the deletion on that location by directly looking into the vcf file, but it is definitely not called.

Best,
Paula

[paulauitt2]

@smolkmo another note: in version 1 I also used the parameter --ignore_sd, but I'm not sure if this has something to do with this problem.