Question: Problem including additional annotations to vcf using snpEff
gravatar for sumudu_rangika
3.7 years ago by
sumudu_rangika30 wrote:


I annotated my vcf files with SNPs using snpEff which has a pre-built database for the species I work on. But my annotated vcf lacks gene product annotations such as whether a particular gene codes for a hypothetical protein etc.

I tried using snpEff -interval option with a gff3 file with gene product information, but got a error saying unrecognized file type. I also have the same information for my species in a gaf file. But snpEff document says -interval command works with txt,bed.bigbed, vcf and gff.

Can anybody provide me a solution to add these additional information to vcf using snpEff.

Thanks With Best Reagrds Rangi

annotations snpeff gff3 • 1.1k views
ADD COMMENTlink modified 3.7 years ago by RamRS30k • written 3.7 years ago by sumudu_rangika30
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