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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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The VG call cannot complete the results #4067

Open HW-Superior opened 1 year ago

HW-Superior commented 1 year ago

Hi, I am using the variation of the vg call sample, the task is done, but the vcf results only have partial results of only one chromosome and no results of other chromosomes, I want to know what causes this? These are my commands: 1.vg construct -t 100 -S -r genome.fa.chr.fa -v all.SV.vcf.gz > graph.vg 2.vg index -t 30 -b ./tmp -x graph.xg graph.vg vg prune -r graph.vg > graph.pruned.vg vg index -t 30 -b ./tmp -g graph.gcsa graph.pruned.vg rm -f graph.pruned.vg 3.vg map -t 20 -x .. /01.ref/graph.xg -g .. /01.ref/graph.gcsa -f .. /00.data/15N200_clean_R1.fq.gz -f 15N200_clean_R2.fq.gz > 15N200.gam 4.vg pack -t 20 -x graph.xg -g 15N200.gam -Q 5 -o 15N200.pack 5.vg call graph.xg -k 15N200.pack -a -t 20 -s 15N200 > 15N200_genotypes.vcf

vg version v1.50.0 "Monopoli"

glennhickey commented 1 year ago

You can verify the paths in your graph (to make sure you have all chromosomes) with

vg paths -Ex graph.xg

You can verify the coverage in your pack file (to make sure all chromosomes have mapped reads) with

vg depth graph.xg -k 15N200.pack -b 1000000
HW-Superior commented 1 year ago

You can verify the paths in your graph (to make sure you have all chromosomes) with

vg paths -Ex graph.xg

You can verify the coverage in your pack file (to make sure all chromosomes have mapped reads) with

vg depth graph.xg -k 15N200.pack -b 1000000

I ran these two commands, and I got the results you're talking about.