REF in VCF file is N

[pingxinxing]

Dear hannespetur, hello, I made some mistakes when running graphtyper. My running command is as follows, but the column REF in my VCF file is all N. “graphtyper genotype_sv genomic.fasta Raw.POP.cnv.vcf.gz --sams=Bam.list --region_file=region.txt --output=.Genotyper" the column REF in Raw.POP.cnv.vcf is normal(fig 1),the column REF in graphtyper result is N (fig 2-3),this is the result of all chromosomes. （fig 1)

(fig 2-3)