Open SZ-qing opened 9 months ago
When i add ref-paths, the results is not be changed:
vg giraffe -Z hprc-v1.1-mc-grch38.gbz -p -f ./small_sim.fq -o json --max-multimaps 10 --ref-paths ./all_graph_paths.txt >small_sim_aln_M10_allpaths.json
I don't know of any tool that does exactly what you're describing. However, the --ref-paths
is only relevant for SAM/BAM output, so it's expected that it would not affect the GAM. If you want to annotate the path position in the GAM, you can use vg annotate -x hprc-v1.1-mc-grch38.gbz -p -a
, but this method definitely has some failure cases. Also, it will only work to annotate positions on reference paths, so you will not get positions for other haplotypes.
Hi, When I prepare to
align my short reads
to thehuman pan-genome
graph genome, the result is only a path, 1. what I want is to provide meall the sequences
that have a mismatch and full alignment with this reads?exon regions, cds regions or intron
regions, from the results?Shell:
vg giraffe -Z hprc-v1.1-mc-grch38.gbz -p -f ./small_sim.fq -o json--max-multimaps 10 >small_sim_aln_M10.json
Results:![image](https://github.com/vgteam/vg/assets/85827219/a533a1db-5def-4e2e-9680-c51d762bbc49)