SimonaSecomandi

vg call produced an empty VCF file

6

**1. What were you trying to do?** Call variants from read support. **2. What did you want to happen?** Generate a VCF file. **3. What actually happened?** The command have...

vg aument Bus error (core dumped)

3

**1. What were you trying to do?** I was trying to performe the augmentation step before variant calling to call variants from a set of illumina WGS reads that I've...

vg index - error: [write_gcsa_kmers()] size limit exceeded

6

**1. What were you trying to do?** Call variants with vg. I'm trying to align of paired-end illumina reads from different bird individuals to a vg graph generated with the...

Detect when nodes are visited predominantly in reverse, and display them backward, instead of making loads of inversion paths

3

Dear all, In the image I’ve attached, there are some SNPs which are confusing to me (the “convoluted” ones). The paths seems to indicate that those are inversions. Indeed, some...

pod5 merge finished without errors at 73%

2

## Issue Description I run the following command which finished successfully but the log says it merged 53 out of 73 files (73%). `pod5 merge -t 32 pod5/*.pod5 -o pod5merged/PAQ83015_bd9104da_d74a1b29.pod5...

ERROR: Signal 6 occurred. VG has crashed - vg safari crashes with short paired-end reads

5

**1. What were you trying to do?** I am trying to align short aDNA reads against a Minigraph-Cactus pangenome made of multiple chr-level haplotype-resolved genomes using vg safari. I didn't...

vg chunk failed: error[vg chunk]: input path not found in xg index

8

Hi all, I am trying to visualize a small pangenome chunk (368 KB). I have a .vg file and .xg file generated as follows: `vg chunk -t 8 -c 1...