I am trying to generate a graph using variants on chromosome 21 in 1000 genomes data with vg. I have run the below command to generate a graph using vg,
vg construct -t 10 -r hg38_chr21.fa -v ALL.chr21.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased_chr21.vcf >1000g_chr21.vg
Then I run the below command to generate a graph image,
vg find -n 157618 -c 2 -x 1000g_chr21.vg | vg view -dp - | dot -Tsvg -o 1000g_chr21.svg
But I am not able to see any variants in the figure. Only what I can see is a stretch of edges with nodes. Please help me to figure out the issue here?
vg construct chops nodes to 32bp by default. vg find -c2 will pull up to 2 nodes on either end of the query. So you are pulling up to 5*32=160bp along the reference path here centered on node 157618. It can be that there is just no variation in the graph there.
You can go hunting for variants by finding one in your vcf, then using vg find -p <chrom>:<coordinate> to find that particular variant's position in your graph.
Finally, vg stores sequence in nodes and not edges. So the display your are seeing is, in all likelihood, 5 nodes connected by 4 edges.