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Hi Bhakti,
The tool in our SNP and Variation Suite (SVS7) software that allows you filter out known SNPs uses matching criteria between the annotation information of your dataset and the data contained in the probe track. The most recent track we have available for this tool is the SNPs 137 track which was created using the downloadable file from NCBI.
For the most basic options available for the tool if chromosome# and position information for a particular marker in your data matches a probe in the track then this is considered a match and if filtering is selected the marker in your data will either be kept or removed depending on user selected filter parameters.
There are also options for more stringent matching criteria, one option available is to match only when alleles of the genotype columns match the alleles for the probe in the track. There is also a matching option for InDels which requires a reference allele field in the marker map of your dataset. You can find more information about this tool in our online manual at the following link. SVS Manual
With SVS we can only annotate using provided downloads from the database sources so these tracks may not contain the most up-to-date information that can be available directly from the source. So it is always possible that the tool in SVS will not find an rs# associated with a particular variant call but that one exists.
Please let us know if you have any more questions.
Thanks, Jami...
