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Question: RefSeq Annotation using SnpEff
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gravatar for preetipankajakshanpillai
20 months ago by
preetipankajakshanpillai • 0
preetipankajakshanpillai • 0 wrote:

Hello,

I am working with human whole genome sequence. I have called variant using samtools and I have annotated my VCF file using SnpEff. In the resultant file I have got only the Ensembl gene and transcript IDs. According to SnpEff documentations, SnpEff supports RefSeq as well, but I am not getting any RefSeq gene or transcript ID. How can I annotate my VCF using SnpEff so that I will get RefSeq gene and transcript IDs for individual variants? Please, help me with this.

Thanks, Preeti
snp ngs snpeff • 1.9k views
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modified 20 months ago • written 20 months ago by preetipankajakshanpillai • 0
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gravatar for preetipankajakshanpillai
20 months ago by
preetipankajakshanpillai • 0
preetipankajakshanpillai • 0 wrote:

Hello all,

I found the solution for the above. I downloaded the complete set of genes and their RefSeq IDs from UCSC website in text format. Copied whole genome sequence (reference), in fasta format, to the same folder. Edited my existing human database (GRCh38) in SnpEff using the following command:

java -jar snpEff.jar build -refSeq -v GRCh38.86 (Note: I am using .86 version).

After editing, annotated my VCF file to obtain resultant file with RefSeq ID instead of Ensembl Ids.

For detailed explanation, go through http://snpeff.sourceforge.net/SnpEff_manual.html#databases , Building Database.

Thanks, Preeti

ADD COMMENT • link written 20 months ago by preetipankajakshanpillai • 0
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