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  • SharonCox
    Junior Member
    • Oct 2012
    • 4
    #1

    Low complexity regions

    I would like to ask the community is it a correct procedure to filter out variants that are called within low complexity regions(I used GATK standard procedures to call variants) ? I am now filtering this exome seq data of multiple affected individuals within families. I noticed that these variants within low complexity regions sometimes co-segregate with the affection status.....are these variants artefacts or are they real ????
    Tags: None
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    Just for the first part of your question. One possibility is to use a BED file(s) for the "repeat" group (repeatmasker etc) from UCSC table browser to identify/filter out variants that lie in those regions.

    Comment

    • SharonCox
      Junior Member
      • Oct 2012
      • 4
      #3
      but is it conceptually correct to filter those variants out anyway?

      Comment

      • GenoMax
        Senior Member
        • Feb 2008
        • 7142
        #4
        Hopefully someone more knowledgeable would be along to answer that part.

        Comment

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