Closed dKlee99 closed 2 years ago
Hi,
I have vcf produced by sniffles for SV calling and tried to annotate it with GFF but it produced an empty output. The below is the bash command I ran.
vcfanno ./references/chm13.draft_v1.1.gene_annotation.v4.gff3 ./longread/samtools/T15/T15_chm13.vcf > vcfanno_annotated.vcf
Your help is very much appreciated!
vcfanno takes a conf file that indicates the files and columns, not a gff. you should see an error message if you run like this.
Hi, thanks for your reply! It didn't show any error messages
Hi,
I have vcf produced by sniffles for SV calling and tried to annotate it with GFF but it produced an empty output. The below is the bash command I ran.
vcfanno ./references/chm13.draft_v1.1.gene_annotation.v4.gff3 ./longread/samtools/T15/T15_chm13.vcf > vcfanno_annotated.vcf
Your help is very much appreciated!