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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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How do we get the imm_regions file? #113

Open prans-neuro opened 7 months ago

prans-neuro commented 7 months ago

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 commented 7 months ago

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).

On Thu, Dec 7, 2023 at 12:29 AM prans-neuro @.***> wrote:

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)?

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