Where to download Normal exome bam for creating PoN (Panel of Normals) for cancer CNV workflow
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6.2 years ago

Hi,

We are trying to get the copy number variation of the tumor only samples (from bam files) using the below workflow (not having paired normal samples)

https://gatkforums.broadinstitute.org/gatk/discussion/9143/how-to-call-somatic-copy-number-variants-using-gatk4-cnv

and for preparing the PoN we plan to use the workflow in below link

https://gatkforums.broadinstitute.org/gatk/discussion/6791

Where do we download or get the normal samples (bam files) for creating the PoN (Panel of Normals)? If we have only one normal sample data (whole exome), can we use it instead of using more that one because the coverage is whole.

Can we use the normal exome data from this link https://github.com/genome/gms/wiki/HCC1395-WGS-Exome-RNA-Seq-Data.

(or)

Can we use the exomes from the the 1000 genomes website for preparing the PoN. http://www.internationalgenome.org/data-portal/sample

Thanks Dr. Prabhakar

copy number variation • 4.0k views
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Karma while it is appreciate that you contribute, please be smart about your answers. You link the data portale from IternationalGenome, which 100% the link OP already posted. The EBI Dataset link is just a portal, this does not answer the question which data OP should use. Will move this to comment.

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