how to get path IDs from vg call with snarls
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5 days ago

My pangenome graph was constructed using minigraph and then was used to call structure variants using vg giraffe. The comands were as follows: vg view -F pangenome.gfa --threads 100 > pangenome.vg vg mod -X 256 pangenome.vg -t 100 > pangenome.mod.vg vg autoindex --workflow giraffe -r ref.fa -p pangenome.mod -g pangenome.mod.vg -t 100 vg chunk -x pangenome.mod.giraffe.gbz -M -O pg -t 25 vg snarls chunk_chr1H.pg > chunk_chr1H.snarls

vg giraffe -Z pangenome.mod.giraffe.gbz -m pangenome.mod.min -d pangenome.mod.dist -f fq1.gz -f fq2.gz -t 40 > sample.gam vg gamsort sample.gam -t 15 -i sample.sorted.gam.gai > sample.sorted.gam vg chunk -x pangenome.mod.giraffe.gbz -g -a sample.sorted.gam -c 1 -t 15 vg pack -x chunk_chr1H.pg -g chunk_4_chr1H_0_516505931.gam -o chunk_chr1H.pack -t 15 vg call chunk_chr1H.pg -r chunk_chr1H.snarls -k chunk_chr1H.pack -s sample -a -t 15 > sample.chr1H.vcf

The first variant information was the follows: chr1H 9358 >293>306 CTGCTGTGATTCGTACTTTCCGGACACCCTAGGTTCCGGTTACGGGGAACTTGTCAAAACTCATAGTTTTGGCCTATTTCGGCTAGTTTTGTATGCTATTAGTCACTAATTTTGGGTCCCGTCGCCATCCGAACATTTTCGGAATCTCGGGGTCCGGTTAAGGGGAAATCATGAAAACTCGTAGTTTTGGCCTATCTCGGCCAGTTTTGTATGCTATTACTCACTGATTTTGGTTCCCACTGCGATCCAAACGTTTCGGGAACCCCGGGATCCGGTTACGGGGAACTCCTCAAAACTCACAGTTTTGGTCTATTTTGGCCAGTTTTGTATGCTATTACTCACTGATTTTGGGTCC C 278.732 lowdepth DP=5415;AT=>293>294>295>296>297>298>299>300>301>302>303>304>305>306,>293>306

I want to know the mean of number of the ID column and INFO column, such as 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306. Are these snarl numbers.

More important, how to know the corresonding path numbers in pangenome.mod.vg file associated with snarl numbers.

vg • 66 views
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