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eldariont / svim-asm

Structural Variant Identification Method using Genome Assemblies
GNU General Public License v3.0
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Calling SNPs with svim-asm? #13

Open cgroza opened 2 years ago

cgroza commented 2 years ago

Hi, I see that svim-asm does a genome to genome alignment to detect SV calls. Is there any reason it could not also list the substitutions in the output VCF file?

jakob-he commented 2 years ago

Hi @cgroza,

At the moment were are not planning to add SNP calling to SVIM-asm. Even though it would be possible based on the genome to genome alignment it would require adding an entirely new use-case/variant-calling approach to the method. Since there are already many other sophisticated algorithms for this purpose available we have not yet seen the advantage of adding it to SVIM or SVIM-asm.

Best, Jakob