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Flagging variants

asked 2012-10-01 11:21:15 -0600

Jeremy Parker gravatar image

Is there/can there be a way to flag false-positive variants seen in GenomeBrowse so that SVS ignores those variants in other analyses?

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answered 2012-10-05 13:09:19 -0600

Sam Gardner gravatar image

There are, of course, many ways such a thing could be accomplished. The simplest way I can think of at the moment, would be to utilize a future feature. We are already planning to implement some variation of user defined 'bookmarks' in genomic space. These would be organizable to some extent and exportable in one or more formats which may be useful elsewhere. Once that feature has been implemented, we could conceivably write a script for SVS to read the exported 'bookmark' list (your flagged variant list, in this case) and mask all intersections in one or more spreadsheets of your choosing.

In short, your procedure would be:

  1. Mark variants in GenomeBrowse
  2. Export the marked variant list
  3. Run the masking tool in SVS
  4. Run analyses on the masked data
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Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.


Asked: 2012-10-01 11:21:15 -0600

Seen: 1,620 times

Last updated: Oct 05 '12