Help with VG Toolkit: VCF Output is Empty

Question

[sarumonsus]

Hello BioStars Community,

I'm currently working with the VG toolkit to analyse genomic data and have encountered an issue where my VCF output (the sample_gam.vcf file) has no variants, despite expecting variants. I'm using VG version 1.52 on my HPC, in which I execute using Singularity.

Here's an overview of the workflow I've run so far. Each generic filename in the commands represents an actual file:

-----------------Generate VG-------------------

singularity exec vg.1.52.sif vg autoindex --workflow map --prefix AllRefGraph --ref-fasta Ref1.fasta Ref2.fasta Ref3.fasta Ref4.fasta Ref5.fasta Ref6.fasta Ref7.fasta Ref8.fasta Ref9.fasta Ref10.fasta Ref11.fasta Ref12.fasta Ref13.fasta Ref14.fasta Ref15.fasta Ref16.fasta

-----------------MAPPING VG-------------------

singularity exec vg.1.52.sif vg map -d /AllRefGraph sample_1.fastq.gz -f sample_2.fastq.gz > sample.gam

---------------CREATING PACK-----------------

singularity exec vg.1.52.sif vg pack -x /AllRefGraph.xg -g sample.gam -Q 1  -o sample.gam.pack

---------------CALL ON VG-------------------

singularity exec vg.1.52.sif vg call /AllRefGraph.xg -k  sample.gam.pack > sample_gam.vcf

I've also tried different commands and workflows from this BioStars post (empty vcf from vg call), but the resulting VCF remains empty.

If anyone has suggestions for debugging or refining my workflow, I would really appreciate your advice!

Thanks in advance!

[Jordan M Eizenga]

What do you get if you use vg stats -a on the GAM file?