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gnomAD in VQSR
I am not sure why no one asked this before but I need help please as I couldn't find sufficient info:
Is it recommended to use gnomAD variants database as known, training and truth set with VariantRecalibrator tool?
If yes, what is the proper prior value then? And is it OK to use the same for the INDEL mode?
Also, in our settings, we extend the sequence just beyond the exons, is it proper to use the exon variants database? Or is it better to use the genome variants database?
I appreciate your help