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