In the genotype_sv result, the REF filed is N, and the ALT filed is not a sequence.

[tanger-code]

Hi.
I'm genotyping SVs in the HG002 sample. The command I used is

for i in {1..22}
do
  $graphtyper genotype_sv $ref_file_folder/GCA_chr${i}.fa  $vcf_folder/chr${i}_sv/chr${i}.vcf.gz --sam=$bam_file_folder/chr${i}_surject_chr_sort.bam --region=chr${i} --output="graphtyper_chr${i}" &
done
wait

The fasta file I used is : GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz.
The vcf file is from : T2TQ100_draftBenchmark.
And I split them up at the chromosomal level.

But the result VCF has some error.
In some records, the REF filed is N, and the ALT filed is not a sequence:

Why does this happen？The fasta file is not N in the corresponding position.