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the problem about 'vg surject+samtools'

7

I'm very sorry to bother you. I used 'vg mpmap' to get a '.gamp' file, and then I tried to project down to linear reference. The code like this: vg...

xuxingyubio

Invalid Haplotype Field Error During pggb to gbz Conversion Due to Incorrect Regex in P-line

1

**1. What were you trying to do?** I was attempting to convert a pggb pangenome graph to gbz format for use in Giraffe. **2. What did you want to happen?**...

sloth-eat-pudding

Questions about read alignment in GAM and BAM format

8

Dear developers: Hello and recently I was using VG to make a variant graph of a plant species and I want to compare the number of reads of one accession...

b524198065

Hi I have vg v1.50.1 "Monopoli" I producing a graph from PGGB and would like to clip off dangling edges where coverage is less than 2 nodes. I'd like to...

brettChapman

When I use `vg call -T` to get the gaf file of each **snarl's traversals path**, I find that it does not contain **all combinations**. Does the file contain only...

tanger-code

vg paths returns no results and no error when using -S and -G together

3

**1. What were you trying to do?** I am trying to use vg to extract the non-reference paths from the Minigraph-Cactus (version 2.6.7) pangenome. I used the command ``` vg...

hui-liu

vg call to GVCF

1

I have a population of 200 individuals, and I know that I can generate VCFs using VG calls. But I want to know how to merge the generation into GVCF,...

biopig

vg call - Segmentation fault (core dumped)

6

Hi VG teams I am copying a post from BioStars where I explain my process in more details but it was suggested to post the bug here. [Here ](https://www.biostars.org/p/9572983/#9573908) is...

nklspp

Normalize snarls

2

Robin-Rounthwaite

Mapping very short reads with vg giraffe

5

Hi vg team! I'm trying to use **vg giraffe for mapping very short paired-end reads (36bp) against a pangenome**. I tried running this command line ``` > vg giraffe -M...

gamerino