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tools for working with genome variation graphs
**1. What were you trying to do?** Hi, I was trying to run `vg map` on the cactus_yeast data, provided here: https://courtyard.gi.ucsc.edu/~anovak/vg-data/cactus_yeast/chroms/ **2. What did you want to happen?** I...
**1. What were you trying to do?** I am trying to use giraffe to genotype structural variants. **2. What did you want to happen?** **3. What actually happened?** The number...
I have constructed graphs previously without encountering this issue. Any ideas or solutions? Thanks in advance. My command looks like this: `vg construct -r ref.fna -v sample.vcf.gz > sample.vg` And...
**1. What were you trying to do?** mapping short reads to a graph with giraffe and call variants **2. My command lines were as below, no other error happened before...
**1. What were you trying to do?** Generate a VCF from the read support. **2. What did you want to happen?** Generate graph_calls.vcf containing information **3. What actually happened?** The...
terminate called after throwing an instance of 'xg::XGFormatError' what(): XG index file version 16 is too new to interpret (max version = 15) ERROR: Signal 6 occurred. VG has crashed....
**1. What were you trying to do?** Get (and understand!) a packed coverage table from an alignment generated with GraphAligner against my variation graph. I have a set of reads...
Hi, I apologize in advance for the lack of code examples but I have to estimate computational resources before starting the project and I was hoping to get some guidance....
**1. What were you trying to do?** View distance index construction progress using `vg index --progress`. **2. What did you want to happen?** Have progress updates written to stdout/stderr. **3....
Hello! I am trying to use giraffe to genotype structural variants. The commands I used for the constructions: vg autoindex --workflow giraffe --prefix Gh -R XG --ref-fasta $ref --vcf $vcf...