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eldariont / svim-asm

Structural Variant Identification Method using Genome Assemblies
GNU General Public License v3.0
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Option to output insertion/deletion coordinates in query sequence? #22

Open cizydorczyk opened 1 year ago

cizydorczyk commented 1 year ago

Is there an option to output the coordinates of an insertion or deletion in the query sequence?

For example, if I wanted to investigate the genes present in a 5kb insertion, I would have to go back to my query contig and look at the annotations in that region. Is there a way to get svim-asm to output such coordinates? I see it can output query names, which I believe would at least tell me which contig if the assembly consists of multiple, but I have not found anything re: coordinates.

Thank you, Conrad

clemgoub commented 2 months ago

Hi there, I am asking myself the same question. I am calling SVs with svim-asm and would like to be able to project the VCF coordinate to each query (alternative) genome. The goal is to make a gff for each genome.

I see the question was also asked here https://github.com/eldariont/svim-asm/issues/11 and here https://github.com/eldariont/svim-asm/issues/14. But I don't think this was resolved. I understand this may not be a priority for the devs, but if someone in the community as come with a nice solution I'll be happy to try!

Before I reinvent the wheel (I'm thinking cross-mapping the flanking regions), I was wondering if we could get this info from SVIM itself.

Cheers,

Clément