WGS hg19/hg38 Panel-of-Normals (GATK SV-CNV)

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3.7 years ago

cocchi.e89 ▴ 260

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!

gatk PoN Panel-of-Normals CNV SV • 1.7k views

ADD COMMENT • link 3.7 years ago by cocchi.e89 ▴ 260

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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 REPLY • link 3.7 years ago by German.M.Demidov ★ 2.9k

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

ADD REPLY • link 3.7 years ago by Kevin Blighe 87k

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