Annovar And String Problems

Question

[Thomas]

I have identified 1000s of SNPs in my study sample (by exome-sequencing). I would very much like to know which SNPs are part of db132.

ANNOVAR is excellent for this purpose; however, it seems that if the alleles in my data does not fit with the ANNOVAR downloadable SNP-data, it treats the SNP as novel, even though the chr and position is correct.

Is there a way to match by only using chr and position? Should I use other annotation programs?

Thanks a lot for helping me out.

The command I use in ANNOVAR: ./annotate_variation.pl -filter -dbtype snp132 mySNPs humandb/

best wishes Thomas

[Sean Davis]

In what format are your variants after exome sequencing? Have you looked at the convert2annovar.pl script that comes with ANNOVAR?

[Thomas]

Thanks for the comment. I actually only have the summary results. Which means that I have the chr, the pos, the minor/major alleles. My problem is that ANNOVAR assign some of my SNPs as novel because my major/minor does not always fit with db reference. It makes sense why the program acts that way. So my Q is. Is there a program that only match on chr and pos.

Answer 1

[Doctoroots]

A possible solution is using the region annotation option in Annovar. basically, treating the dbsnp file as a region file will result in location comparison without considering the alleles.

the command will look like this:

annotate_variation.pl -regionanno -dbtype snp132 -buildver hg19 mySNPs humandb/

if that doesnt work, try converting the dbsnp132 file into a bed file and using the -bedfile option.

[Thomas]

Yes.... perfect. Spot on. Thanks

I must admit that I used another solution since the question is rather old.