Need some input from the community concerning the question in title -
Some of the SNPs deposited in dbSNP database were later removed due to mapping or clustering errors - for example rs11273140 (which you would find nothing using NCBI or Ensembl, one record in 1000 genomes browser, which states the rs is deleted).
If this rs is removed in dbSNP due to mapping/clustering errors, what does it mean when my VCF file reports such a variant in my sequencing cohort ?
(a) there is a mapping/clustering error during my sequence alignment (not using an updated ref seq? not using an updated dbSNP list? other possibility? ) (b) sequencing platform issue (e.g. exome seq v whole genome seq seem to report different SNPs) (c) others?
Any insight/reference will be appreciated. Thank you.