Using VG to extract path sequences/sub-sequences

Question

[Andy Yates]

Hi there. I'm looking into adapting refget into something that can work with graph genomes and not just linear genomes. Specifically I'd like to extract the sequence of a full path and subsequence of a path given a path identifier. I've spent this afternoon dipping in and out of vg and other related tools and believe this is possible but I'm just not seeing how. Is this possible? If so would I need to look into coding something custom or is there a vg command that could do this?

Thanks in advance

Answer 1

[glenn.hickey]

There's no interface to do that exactly. You can get a whole sequence with vg paths -F. You can get part of a sequence with vg chunk -x graph.vg -p chr10:200-300 -c 0 -E range.bed | vg paths -F -Q chr10 -v -`

But the sequence returned will be rounded to the nearest graph node. So it may actually be, say, 180-400, which would be written in range.bed above. So you'd need to put that through samtools faidx to get the exact range you want. Very clunky, but doable in theory I guess.