which is more reliable Annovar or SnpEff

[msorianoc]

Hi.
I sequenced a human exomes and I echo with the annotations and Annovar SnpEff. But the results are quite different and I do not know where to stay. Any suggestions?

Thank you.

[jxchong]

I would first look to see what gene model you are using for the annotations. Are you using Refseq with both programs? Or is one using Refseq and the other using CCDS/Gencode/other? Are they using the same version of Refseq?

That probably explains the vast majority of differences!

[msorianoc]

Thanks for your comment, Yes, I'm using the same version of RefSeq.
I use hg19, dnsnp135
SnpEff version is the version 2.0.5d and is Annovar April 2012

[NGSfan]

They are different in what respect?

Are they reporting different locations of variants in the CDS transcript? Or are they different on the nucleotide/amino acid changes?

Or there are more annotations in one versus the other?

Would like to know as well.

[msorianoc]

The main difference is that there are many more entries than Annovar SnpEff. There are also annotations Annovar SnpEff not appear. The annotations that appear in both no nucleotide changes.

[jxchong]

The main difference is that there are many more entries than Annovar SnpEff. There are also annotations Annovar SnpEff not appear. The annotations that appear in both no nucleotide changes.

I don't understand what you mean? Do you mean there are many more entries from Annovar THAN from Snpeff?

Can you give some examples?

dbSNP135 is not the same as Refseq. Which Refseq versions are you using?