Hello everyone! I am using a pipeline which performs tumor-normal matched analysis. As output, it gives the VCF and Excel files only for somatic variants, excluding germline.
As I need to have those germline variants in the file for further annotation, I have performed a script to add those absent germline variants in the excel file.
What I would need is to create a new vcf file from the data on that excel file. Is that possible?
I have been trying VariantAnnotator from Bioconductor and pysam and pyVCF in python. I couldn't find how to create one from scratch, but it reads already created vcf's. Any help, ideas, tips is more than welcome!