I’m trying to create the gnomadFreq.tsv file for the priors needed to run the de_novo function on a vcf file that has trio calls.
What is a way to create this file and what format does it have?
the thing you need is not a file, but a variant annotation that is the population frequency. Do you have something like that? Using the gnomad frequencies from gnomad.broadinstitute.org may be a good idea.
Thank you for the help.
I’m running Hail after GATK best practices, and using just one trio so I guess I’d have to annotate with gnomad, but can’t find a way to do that from the tutorials.
In that case, this algorithm may not be the right one – it’s designed to work on cohorts, where there’s information from looking at frequencies across all your samples.
If think if you just set that parameter to 0 you’ll get mostly the results you expect, though the HIGH / MEDIUM / LOW confidence in calls should be taken with a grain of salt.