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
#CHROM POS ID REF ALT 10 3978708 rs29320259 C T
#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