Attention: Want an end-to-end pipelining solution for GATK Best Practices?
Calling Somatic Variants without matched normals using GATK.
I am new to the world of bioinformatics. I currently have sequencing data (WES) of about 45 pediatric brain tumor samples (archived FFPE), I am keen on identifying mutational burden and mutational signatures in these samples. I don't necessarily
want to discover a novel mutation and describe it's biological relevance. More use the pattern of mutational signatures to identify the causes of recurrence in tumors. The problem is like with most archived FFPE samples I don't have matched normal tissue. I am looking at the best approach to call somatic variants in these samples. Is Using gnomAD for filtering my best option? Is that a good resource for pediatric tumors? If no then what could be other potential sources for this.
Thank you for your advise.