Question: Annovar And String Problems
1
gravatar for Thomas
9.3 years ago by
Thomas730
Copenhagen, DK
Thomas730 wrote:

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

annovar snp annotation • 2.1k views
ADD COMMENTlink written 9.3 years ago by Thomas730

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

ADD REPLYlink written 9.3 years ago by Sean Davis26k

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.

ADD REPLYlink written 9.3 years ago by Thomas730
1
gravatar for Doctoroots
8.7 years ago by
Doctoroots790
Doctoroots790 wrote:

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.

ADD COMMENTlink written 8.7 years ago by Doctoroots790

Yes.... perfect. Spot on. Thanks

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

ADD REPLYlink written 8.7 years ago by Thomas730
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