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How to identify Denovo Mutations in the child compared with parents?
I am new to NGS analysis and have been following this pipeline recommended in many of the posts in the online forums. I have 3 samples(1 child, 2 parents) and completed analysis till generation of VCF files using HaplotypeCaller. I would like to find de novo mutations in the child, Is it a good idea to proceed for de novo mutations identification after annotation or before annotation? Please advise me on how to proceed with this ?
Note: This question has been asked in another forum but I didn't get suggestions on the GATK functions.