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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
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empty output #145

Closed dKlee99 closed 2 years ago

dKlee99 commented 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 image

Your help is very much appreciated!

brentp commented 2 years ago

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.

dKlee99 commented 2 years ago

Hi, thanks for your reply! It didn't show any error messages