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

Hi,

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 • 900 views
ADD COMMENTlink modified 2.8 years ago by RamRS24k • written 2.8 years ago by sumudu_rangika30
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