Question: MAF threshold in The Cancer Genome Atlas (TCGA) and Personal Genome Project (PGP)
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gravatar for fatmasayed93
11 months ago by
fatmasayed930 wrote:

I am studying the minor allele frequency (MAF) over different datasets. Geneticists used to exclude SNPs with MAF under certain small values. In big databases and projects like 1000 genome-project (MAF=0.01) and HapMap-project (MAF=0.05), they've mentioned the value of the MAF threshold. I want to know the values of the MAF threshold adopted in The Cancer Genome Atlas (TCGA) and Personal Genome Project (PGP).

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ADD COMMENTlink modified 11 months ago by Kevin Blighe65k • written 11 months ago by fatmasayed930
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gravatar for Kevin Blighe
11 months ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

For PGP, please inquire direct to the UK team at UCL: https://www.personalgenomes.org.uk/

For the TCGA, I am not sure that minor allele frequency was used for the purpose of filtering somatic variants. Please check the materials and methods of the published works relating to TCGA data.

Kevin

ADD COMMENTlink written 11 months ago by Kevin Blighe65k
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