Annovar snp131 rs-number annotation

[oyvindbusk]

Hello all,

I am testing Annovar, which is a great piece of software. I have encountered a small glitch, however, and were hoping someone else has had the same trouble (and solved it). When annotating with the -geneanno option, I do not get my data annotated with rs-numbers. Therefore, I am trying to get the following command to work:

annotate_variation.pl [B]-dbtype snp131[/B] infile.ann humandb/ -buildver hg19

In order to do that, I was asked by the program to download the snp131db by issuing the following command:

annotate_variation.pl -downdb snp131 humandb/ -build hg19

The download and extraction worked fine, but when running the above command, Annovar reports that it doesnt recognize the format:

NOTICE: Reading gene annotation from ../../pipeline/annovar/humandb/hg19_snp131.txt ... Error: invalid record found in ../../pipeline/annovar/humandb/hg19_snp131.txt (chrom field not found): <585     chr1    10433   10433   rs56289060  0+       -       -       -/C     genomic insertion       unknown 0       0       near-gene-5     between 1>

I find this rather strange, but perhaps anyone else has also seen this?

Best regards,
Øyvind

[adamyao]

For variant annotation of human genome, would you like to try using VarioWatch to see it fits your needs.

http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do

Adam

[ulz_peter]

I guess the -build hg19 is just a typo is it?
It is supposed to be -buildver hg19
but if the rest works fine, that can't be the problem.

[oyvindbusk]

Hi,
Thats a typo, although I think -build will also work for the downdb-option.

However, the author of the program kindly pointed out that for snp annotation, I need to use the -filter option, and that solved the issue.
-Ø