Question: Creation of a large Panel of Normals for Mutect2 analysis
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gravatar for filippo.martignano
16 months ago by
filippo.martignano10 wrote:

Hi everyone.

We are thinking of generating a large Panel of Normals (PON) from TCGA samples for Mutect2 analysis in Cancer Genomic Cloud (CGC genomics). Our idea is to create a PON with as many blood normal samples as possible through the latest Mutect2 version (possibly the final version 4.0). There are 9244 Blood Derived Normal WXS bam files in TCGA, and generating a PON from such a large sample set requires storage and calculation power that could be challenging for a single lab. Since we noticed multiple threads from people struggling to obtain a large and reliable PON, we thought some of you could be interested in making a PON in collaboration with us. One option could be to apply together for one of the grants provided by CGC in order to generate a ’standard’ PON (for additional information about CGC grants: http://www.cancergenomicscloud.org/free-credits/). Alternatively every workgroup could perform part of the analysis (locally or on CGC) and then join together the VCFs in one single PON. If you are interested please let us know via this thread. If we reach an adequate number of interested people, we will see what can be done and how to proceed (eg which samples could be used and how to divide the analysis). Of course, everyone interested must have a regular access token to TCGA controlled data.

ADD COMMENTlink modified 6 months ago by lixuenan20080630 • written 16 months ago by filippo.martignano10
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gravatar for lixuenan200806
6 months ago by
lixuenan20080630 wrote:

Hi,has standard Panel of Normals (PON) file been created for GATK4 mutect2 ? I am interested in this file

ADD COMMENTlink written 6 months ago by lixuenan20080630
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