Get annotation scores from dbsnp rsids

Question

[ranjak1]

I have a list of dbSNP rs ids and I would like to get scores for the 16 or 17 annotation tools as used by annovar. When I run annovar on these rsids. I get a lot of missing values rows (around 16k out of a list of 20k). Is there any way I can get these annotation scores with minimum fuss.

Answer 1

[Emily]

Sift and PolyPhen are only for missense variants that alter the amino acid sequence. Are all your variants missense?

[ranjak1]

Thanks for pointing that out I checked and they werent.

[ranjak1]

If some snp has two possible substitution in the amino acid sequence does that mean there will be two SIFT scores for that snp