Calling Germline SNVs

6 important questions on Calling Germline SNVs

Silent (Synonymous) mutation

Single base substitution that does not change that sequence of the protein. Leaves protein as it is.

Nonsense (truncating) mutation

Single base substitution introducing a (premature) stop codon. Leads to a truncated protein.

How to call somatic mutations?

Align tumor sample to reference sample, find differences
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But why call germline mutations?

  • Genetic predisposition
  • If you don't know germline mutations, all mutations are somatic
  • Quality check with multiple samples prevents sample swap
  • Build noise models that improve somatic calling methods
  • Refine compy number calling

What can look like a sample swap?

A bone marrow transplantation

How to call germline mutations?

Genome Analysis Toolkit (GAT)

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