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[odgi::extract] error: the node IDs are not compacted. Please run 'odgi sort' using -O, --optimize to optimize the graph
However, when I use the optimized graph, it of course has different node IDs than the original input gfa. This is a problem as I have a vcf containing node IDs from the unoptimized graph, and I want to be able to cross-reference between the subgraph and the vcf. Is there any way to do this? Thanks!
The text was updated successfully, but these errors were encountered:
I'm trying to extract a subgraph like so:
odgi extract -d100 -r'genome1#chr1:11159196-11400464' -o out.og -i pangenome.og
but receive the error
However, when I use the optimized graph, it of course has different node IDs than the original input gfa. This is a problem as I have a vcf containing node IDs from the unoptimized graph, and I want to be able to cross-reference between the subgraph and the vcf. Is there any way to do this? Thanks!
The text was updated successfully, but these errors were encountered: