Is This An Error Of Ref Dbsnp?

Question

[Tonyzeng]

HI, I generated my own samples' variant or SNP calling table and plan to narrow down or filter these many of the variants using dbSNP. Here i downloaded two dbSNP with one from NCBI and another from Sanger. However, I doubt NCBI one has error when it called a nt variant change from C to T (see belows). IF it is a variant from reverse strand, it should be at least A to G replacement. I am so concerned about how many of these kinds of potential error in NCBI dbSNP which could influence my variant/mutation filtering?

Anyone has suggest on this? thank you

NCBI dbSNP

#CHROM          POS               ID         REF      ALT
  10         3978708         rs29320259       C           T

Sanger dbSNP

#CHROM          POS                ID         REF      ALT
 chr10         3978708         rs29320259      T        C

My own sample SNP calling

#CHROM                 POS             ID         REF      ALT
chr10         3978708    3978708          .       T           C

Answer 1

[DG]

I see variants like this all of the time. Personally I do my filtering based on minor allele frequency, and not just the presence of a dbSNP id. If there is a dbSNP id with no known minor allele frequency it could be for a variety of reasons. Some of these are problematic regions of the genome and may represent fairly common false positives which you would want to filter out, but many others are simply SNPs that were deposited, often a long time ago, and never seen again in other sequencing projects.