How to further process and annotate VCF files derived from mapping a patient`s whole genome FASTQs to a separate genes GenBank (.gbk) files? I have genome of a patient having medullary thyroid cancer. I have run alignment to a set of 30 genes relevant to cancerogenesis and chemotherapy decision. Some genes have a few mutations, some over a 1000 of them. Now I have 30 VCF files and .csv SNP and INDEL lists. I need to know what to do with these files: should i put them into SNPEfff or there is some proper web service to do annotation? In other words, What processing steps are to be done with these VCF files, is it necessary to filter them, normalize or smth else? Never had an experience with an actual human genome before
Question: How to further process and annotate VCF files derived from mapping a patient`s whole genome FASTQs to a separate genes GenBank (.gbk) files?
16 days ago by
mathisdead • 0
mathisdead • 0 wrote:
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