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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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the sv coords in query genomes #1188

Open wu123tj opened 1 year ago

wu123tj commented 1 year ago

Hi @glennhickey: I have got the vcf result from the minigraph-cactus pangenome pipeline. how can I get the coords of the SVs in the query genomes since there are only coords of SVs in the reference genomes ?

Best,

glennhickey commented 1 year ago

The VCF only contains reference coordinates, so there's no direct way. You can try to use the AT field from the VCF to map back to the graph (with vg find) in order to get the coordinates. This will require converting the .gbz to .xg to work properly (which will require a fair amount of RAM). You can also liftover coordinates directly using the HAL file.