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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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no SVs were called in large gap #509

Closed hjt1129 closed 2 months ago

hjt1129 commented 2 months ago

hi, I compared two assembled genome to find SVs between them, when i open the bam file in igv (see the figure), it possess a large gap between 25700kb to 26000kb, so why the sniffles can not detect it, even if i used --no-qc? is it too long or something else?

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fritzsedlazeck commented 2 months ago

Dear @hjt1129 We would need to know a bit more. What's your coverage? You show here one read I think? That would not be enough to call an SV. To make sure. Please klick on link supplementary files. This should display a thin line between the segments, which indicates that the two segments are actually connected. Otherwise it's just a lack of coverage of one read which would not qualify as an SV.

Thanks Fritz

hjt1129 commented 2 months ago

hi, Yes, it only has one contig because it was the assembled genome that mapped to the reference genome. It shows the same contig (ptg000254l) for the sequence before 25.7k and that after 26.0k. Actually, two SVs (position 25555966 with the SVLEN=10607; position 26071917 with the SVLEN=6138) was also called by sniffles where also has only one read (i.e. the ptg000254l contig). So it's confused me why this large gap can not be called.

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fritzsedlazeck commented 2 months ago

ah so thats whats going on. .. Sniffles is not designed for an assembly alignment. I would recommend using Dipcall for example. Sniffles is for when you have mapped long reads to the reference and want to obtain SV.

Good luck Fritz