How do we get the imm_regions file?

[prans-neuro]

To remove Spurious CNV Calls in Immunological Regions, how does one find the imm_regions files? Does this need to be created, if so, what are the parameters should we consider while using data from hg19 - SNP array (GSA3)?

[kaichop]

You can find such regions yourself in UCSC genome browser. However, it is often not a big issue and you can always address it later (after calls are generated and suspicious CNVs are found in regions with immunoglobulin).

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