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cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
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Not finding 4kb deletion #75

Closed ccbruels closed 9 months ago

ccbruels commented 9 months ago

Hi, I ran NanoVar on a ~20x coverage ONT data set. I noticed that it is not calling a ~4kb deletion (screenshot attached). I can't find a max SV length parameter, is there something I can do to call SV like this? BTW - the reports are very helpful! Thanks! Christine NanovarNotFindingDeletion

cytham commented 9 months ago

Hi @ccbruels, is this hg38? Can you share the genomic coordinate of the deletion?

ccbruels commented 9 months ago

Hi ChengYong,

It is hg38, the deletion is chr10:131592486-131597187. The deletion was called by Sniffles1, Sniffles2, and DeBreak. I noticed the deletion because IGV gave an error message when I tried to load the vcfs from DeBreak and Sniffles2. It can load the vcf with the deletion from Sniffles1, and the vcf from NanoVar which didn't call the deletion.

When I looked at it more closely after writing you, I see that NanoVar is the only one of the 4 callers that called it correctly (in this case NOT calling an SV).

The sequence that was reported as being deleted is composed of a SINE (AluSg) and 2 LINES (L1MB3 and L1PREC2). The initial assembly of hg38 has this same SINE and 2 LINES followed by a very similar AluSg-L1MB3-L1PREC2/L1PA14. There is now a fix (chr10_KN538365v1_fix) which does not include that first AluSg/L1MB3/LiPREC2. This fits with our ONT data which indicates that the first AluSg/L1MB3/LiPREC2 in hg38 is likely not present.

Best, Christine

On Fri, Jan 19, 2024 at 6:33 AM ChengYong Tham @.***> wrote:

Hi @ccbruels https://github.com/ccbruels, is this hg38? Can you share the genomic coordinate of the deletion?

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cytham commented 9 months ago

Interesting. Thanks for sharing this Christine!