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pablo-gar / somatic_mutations_GTEx

Methods and analysis for Garcia-Nieto, et al. Somatic mutations
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How to generate Panel of Normals for the pipeline? #2

Open YingYa opened 4 years ago

YingYa commented 4 years ago

Hello,

I would like to use the pipeline to call somatic mutations from tumor-only RNAseq data. Would you mind to detail that how to generate the Panel of Normals?

Thanks, Ya

pablo-gar commented 4 years ago

Hi Ya,

In this study I used two types of PoN

  1. Tissue-specific PoN
  2. Whole-data PoN

Those were constructed as follows:

Tissue-specific PoN eliminates all mutations that occur at least 40% across samples of the same tissue Whole-data PoN eliminates all mutations that occur at least 4% across samples of all tissues

You can calculate the frequency of unique mutations from a mutation map file using this shell command. A mutation map has to have at least these tab-separated columns: chromosome, position, reference base, mutation. For example: chr1 25451781 G A