I am new to NGS analysis and have been following this pipeline recommended in many of the posts in the forum.
I have 3 samples(1 child, 2 parents) and completed analysis till generation of VCF files. I couldn't understand clearly the VariantFiltration step from GATK documentation. Could someone please give more information on the same ?
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 ?