Low complexity regions

[SharonCox]

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 ????

[GenoMax]

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.

[SharonCox]

but is it conceptually correct to filter those variants out anyway?

[GenoMax]

Hopefully someone more knowledgeable would be along to answer that part.