vg autoindex vg giraffe pggb gfa

[hgz2021]

The vg version I use: version : v1.59.0 I used PGGB to construct a pan-genome (GFA); I want to rely on him to find the SNP of the sample; Here's my current script: vg autoindex -t 5 --workflow giraffe -r fasta -g pggb.gfa -p ./chr1_cute vg giraffe -p -t 5 -d dist -Z gbz -m min -f R1.fastq.gz -f R2.fastq.gz -N SRR -o BAM > SRR.bam The error warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. error:[vg::get_sequence_dictionary] No reference or non-alt-allele generic paths available in the graph! Here's what I would like to ask you: Does VG have any commands or parameters for adding a reference genome to a GFA file? At present, I want to find the SNPs in the second-generation samples through the pan-genome generated by pggb;; If you have any other way to do this, please get back to me. (MC I've used)