vg
vg copied to clipboard
vgteam
tools for working with genome variation graphs
Hello, I am using vgtools deconstruct as: ``` vg convert -g smooth.gfa -p > out.pg vg index out.pg -x out.xg vg snarls out.xg > out.snarls vg deconstruct out.xg -r out.snarls...
This would be a field like `AT` but containing the "stable coordinate" version, ie its range in the original input contig sequence.
Each site is converted independently. In the event of multiple traversals through a site for a given haplotype it just chooses one (I think) and uses it. If there are...
Hello,Professor I have two genomes from two species. My end goal is to construct a graph of the two genomes from two species and then map tens of illumina short...
Dear all, Can I use minigraph+Giraffe to achieve genotyping of structural variants in the framework of the graph genome? Thank you in advance. Sincerely, Zheng zhuqing
**1. What were you trying to do?** I was trying to construct graph using construct module from /test/1mb1kgp fasta and vcf **2. What did you want to happen?** I ran...
**1. What were you trying to do?** I am trying to set up a reference panel using `vg deconstruct -a -g`, followed by genotyping of the reference panel using `vg...
**1. What were you trying to do?** Try to genotype SVs from the short-reads ''' vg call wg.xg -k wg.pack -s QNM -v index/all.vcf.gz -t 10 -r Graph.snarls > TEST.vcf...
@benedictpaten wants Giraffe to be "fully simple". This has two elements, as I understand it: * We should have standards and specs for input formats we want from HPRC, to...
I am trying to use giraffe to genotype structural variants of one chromosome from a mamilian genome. I am following this tutorial. https://github.com/vgteam/vg/wiki/SV-genotyping-with-vg and the commands from this Snakefile https://github.com/vgteam/vg_snakemake/blob/master/Snakefile...
