Question: WGS hg19/hg38 Panel-of-Normals (GATK SV-CNV)
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gravatar for cocchi.e89
6 months ago by
cocchi.e89120
cocchi.e89120 wrote:

I am working on CNV calling through GATK latest guideline, in order to perform the analysis there's need for a Panel-of-Normals file that can be generated from other samples.

I was wondering if it possible to download these PoN files from some repository etc., I'm interested in both hg19 and hg38

Thank you very much in advance for any help!

cnv panel-of-normals pon gatk sv • 347 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by cocchi.e89120
1

Hi,

I believe you can download 1000GP samples or PCAWG samples to do so (1st one is open, 2nd one require applying for an access).

In general I would pay attention to 2 parameters to match between your tumor samples and normal samples - 1) PCR-based or PCR-free sequencing (old samples tend to be PCR-based), 2) insert distance - different insert-distances create quite dissimilar coverage profiles.

ADD REPLYlink written 6 months ago by German.M.Demidov1.9k

Hi, I would ask on the GATK support forum, and link back here when you do that. Thanks!

ADD REPLYlink written 6 months ago by Kevin Blighe69k
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