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• Adding short sequences to a genome graph
  I can create a genome graph based on multiple genomes using `minimap2` for inital alignment and `...
• Issues calling variants with vg when using other tools upstream
  I have a graph of 10 different assemblies of the 5 Mbp salmonella genome created with [pggb](http...
• Short read alignment to pangenome
  Hi, I have a pangenome graph in dot format. I want to align short reads (fastq) to this graph. I...
• vg mapping comparison: graph vs flat graph
  Is there any way to do a vg mapping comparison: Two vg gam files: 1. one from the flat graph con...
• Edit distance of an alignment
  I am new to VG. I have mapped short sequences to a genome graph using *vg map*. Now I wish to e...
• empty vcf from vg call
  Hi I am getting an empty vcf file when I run below commands vg construct -t 10 -r /data/pub...
• Segmentation fault (core dumped) during vg surject
  I tried to run `vg surject` on a GAM file I generated with `vg map`, but the call ended with "Seg...
• how to call variance from vg multiple path alignment "mpmap" .gamp
  Is there any instruction on how to call variance from vg's multiple path map output? I did not fi...
• vg de novo calling strategy
  Hi all, I am not sure I understand correctly how we are supposed to use the vg pipeline when we ...
• Best strategy starting from allelic chromosomes instead of reference plus VCF
  Hi all, I am trying to do genotyping (DNAseq samples) and allele specific expression (RNAseq sam...
• call variants from cactus output
  I am new on vg tools. I have 100+ fungi assemblies and raw reads. The assemblies were aligned by ...
• VG view command hangs with no result (VG Toolkit)
  I'm trying to construct the variation graph as stated in "Working with a whole genome variation g...
• BWA-MEM - Improperly Paired Reads
  After aligning paired-end 100bp reads to a reference genome, I am getting very low properly paire...
• Best way to map paired-end, uniquely mapped reads with Bowtie2?
  This has come up before, but I have never been satisfied with, or completly understood, the answe...
• Whole-genome alignment of two or more bacterial genomes - find structural variants
  Hello, Let's say I have two or more complete bacterial genome sequences produced by Sanger seque...
• Single end or paired end for variant calling
  Hi Biostars, I want to align reads from a non-model microbat genome to the repeat-masked version...
• How to solve `obj/haplotype_indexer.o error` when i `make static`.
  My operating system is CentOS, my CPU that supports SSE 4.2 and, GCC version is 5.3.0. I have sol...
• Merging .gam files
  Can anyone point me towards a method to merge gam files that are created by using ' vg map ' to ...
• supporting vg users on biostars
  I'd like to announce that we'll be using this forum as a way to provide support to users of [vg](...
• Too low recall for insertion
  Dear developer. I am working on measuring the sv calling performance of vg software using nanopo...