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Old 10-16-2014, 04:22 AM   #1
SharonCox
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Default 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 ????
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Old 10-16-2014, 05:35 AM   #2
GenoMax
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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.
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Old 10-16-2014, 07:18 AM   #3
SharonCox
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but is it conceptually correct to filter those variants out anyway?
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Old 10-16-2014, 07:25 AM   #4
GenoMax
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Hopefully someone more knowledgeable would be along to answer that part.
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