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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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genes in structural variants #2969

Open terestahl opened 2 years ago

terestahl commented 2 years ago

When listing genes included in structural variants what is the order the genes are listed? would it be possible to keep the genomic order instead? this will be much more useful specifically to be able to identify the genes involved in the breakpoints

An example of what I get after downloading using the "Filter and Export" tool from scout

SETX | BARHL1 | MED27 | AK8 | TSC1 | DDX31 | PRRC2B | TTF1 | GFI1B | POMT1 | CFAP77 | SPACA9 | NTNG2 | GTF3C4 | RAPGEF1 | UCK1 | EIF4A1P3 | SNORD62B | SNORD62A | RNU7-21P | RN7SL328P | RNU5D-2P

what is the order used????

this is a link to UCSC if you whant to see the genomic order

thanks

northwestwitch commented 2 years ago

Hi! I think genes from structural variants come in the order they were saved in the database for that variant and it's probably not by coordinates. It should be possible but a bit complicated because gene coordinates are not saved inside the variant document at the moment. Example of gene info saved in the variant:

image

In order to get gene coordinates we should query the database for gene coords for each gene belonging to the variant. Could be done but it will slow down a lot the variants download process for variants which contain many genes.

terestahl commented 2 years ago

Ok and it is not possible to re-sort the database by coordinates each time you add new information into it so the genes appear in the right order?

dnil commented 2 years ago

Genes are normally sorted on hgnc_id, and I would assume it's the same here. I do agree it would be a nice feature to show which are closest to the breakpoints for balanced events. We could probably retrieve any gene hit by a breakpoint with fewer queries, but it wouldn't be exactly the same.

northwestwitch commented 2 years ago

Reordering the genes saved in variants document should eventually be done around here in the code: https://github.com/Clinical-Genomics/scout/blob/54809c217a6ce997a3630dabb199f1b09570ef59/scout/build/variant/variant.py#L278

terestahl commented 2 years ago

ok thanks then sorting after genomic position is not an option? It would be more biological relevant anaway

From: Daniel Nilsson @.> Sent: Tuesday, November 9, 2021 4:42:52 PM To: Clinical-Genomics/scout @.> Cc: Teresita Díaz De Ståhl @.>; Author @.> Subject: Re: [Clinical-Genomics/scout] genes in structural variants (Issue #2969)

Genes are normally sorted on hgnc_id, and I would assume it's the same here. I do agree it would be a nice feature to show which are closest to the breakpoints for balanced events. We could probably retrieve any gene hit by a breakpoint with fewer queries, but it wouldn't be exactly the same.

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northwestwitch commented 2 years ago

We are working on some other things at the moment (previous customer requests and maintenance stuff). Let's leave this suggestion open so we can work on it when we have some time and especially if other users are interested in this feature.

terestahl commented 2 years ago

😃👍

From: Chiara Rasi @.> Sent: Wednesday, November 10, 2021 8:44:15 AM To: Clinical-Genomics/scout @.> Cc: Teresita Díaz De Ståhl @.>; Author @.> Subject: Re: [Clinical-Genomics/scout] genes in structural variants (Issue #2969)

We are working on some other things at the moment (previous customer requests and maintenance stuff). Let's leave this suggestion open so we can work on it when we have some time and especially if other users are interested to this features.

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