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Hi,
I would like to compare SNPs from a sequencing project against those reported in dbSNP for specific phenotypes (I am currently using the Biomart service on ensembl.org for this purpose). My goal is to select only SNPs for which the precise location at single base level (not just the approximate genome region) is known. However, to filter the SNPs, I only found the attributes "p-value" and "Validation status", where the validation status field can contain the following values: cluster,freq,doublehit,1000Genome. If I want to ensure that the SNP position is accurate, should I only select SNPs that have actually been sequenced (i.e. validation status contains "1000Genome") or how reliable are the positions reported for other SNPs that were obtained from GWAS (i.e. how can I filter them)?
Thanks for your help.
I would like to compare SNPs from a sequencing project against those reported in dbSNP for specific phenotypes (I am currently using the Biomart service on ensembl.org for this purpose). My goal is to select only SNPs for which the precise location at single base level (not just the approximate genome region) is known. However, to filter the SNPs, I only found the attributes "p-value" and "Validation status", where the validation status field can contain the following values: cluster,freq,doublehit,1000Genome. If I want to ensure that the SNP position is accurate, should I only select SNPs that have actually been sequenced (i.e. validation status contains "1000Genome") or how reliable are the positions reported for other SNPs that were obtained from GWAS (i.e. how can I filter them)?
Thanks for your help.