How can i use several samples of resequencing data to get a visualize paths
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11 months ago
congruisun • 0

Hello vgteam. If I have 10 samples of resequencing data and a reference graph. how can I get a picture like Fig.1? Each line represents a sample.

I want to get the genome graph of the species through vg. Then use the genome graph to compare the variation of each sample and visualize it. I know vg view -d t.vg -A t.gam | dot -Tsvg -o aln.svg can do something similar, but the result is too large to open it. I hope to show it concisely in the form of Fig.1.

vg • 251 views
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Entering edit mode
11 months ago
glenn.hickey ▴ 240

You can make the dot output a bit smaller by passing -S to vg view. You can also subset to a region of interest with vg find -p chr1:500-600 | vg view - pd .... Or you can try the interactive viewer here https://github.com/vgteam/sequenceTubeMap.