Calculating derived allele frequency
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14 months ago
peter ▴ 10

I am reading the following article:

Link to the article

In results and discussion session they say:

We also generated ROC curves showing the models discriminating pathogenic mutations defined by the ClinVar database (Baker, 2012) from likely benign Exome Sequencing Project (ESP; Fu et al., 2013) alleles with a derived allele frequency (DAF) ≥5% (Fig. 1b, n = 10 000 pathogenic/10 000 likely benign).

I have downloaded ESP variant files from the following link:

Link to ESP vcf file

And info column of these vcf files does not have derived allele frequency. It has minor allele frequency. So my question is how can extract variants from ESP file with derived allele frequency greater than 0.05?I am new to bioinformatics therefore, I am sorry if this is super basic question

allele-frequency variants vcf genome ESP • 375 views

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