search

broadinstitute / genetic-prevalence-estimator

https://genie.broadinstitute.org/
BSD 3-Clause "New" or "Revised" License
1 stars 0 forks source link

Hide filtered variants by default #96

Closed sambaxter closed 2 years ago

sambaxter commented 2 years ago

I think it is confusing to have the filtered variants which result in a "0". Could we hide those and then have a warning saying some variants not included in list and then have the option to view them? If the filtered variants still have some allele counts we can leave those in the list

nawatts commented 2 years ago

Is this a custom variant list?

We're filtering out variants with an overall AC of 0 in the data pipeline step, so they shouldn't be showing up in recommended variant lists at all.

https://github.com/broadinstitute/aggregate-frequency-calculator/blob/9100d4c0a917d09c1f543ca790589b0815caebc0/data-pipelines/prepare_gnomad_variants.py#L110 https://github.com/broadinstitute/aggregate-frequency-calculator/blob/9100d4c0a917d09c1f543ca790589b0815caebc0/data-pipelines/prepare_gnomad_variants.py#L120 https://github.com/broadinstitute/aggregate-frequency-calculator/blob/9100d4c0a917d09c1f543ca790589b0815caebc0/data-pipelines/prepare_gnomad_variants.py#L166

nawatts commented 2 years ago

These are showing as AC 0 in the calculator because we don't count alleles from exomes/genomes if the variant fails QC filters in that sample set. Some variants are filtered in both exomes and genomes so they show up as AC 0 in the calculator.

Decided that the calculator's AC numbers are fine as is, but we should hide AC 0 variants by default.

nawatts commented 2 years ago

I'm having a bit of trouble deciding what to label this option. "Show/hide filtered variants" doesn't really work since it's not hiding all filtered variants, only those that are filtered to AC 0. Maybe "Show/hide variants that do not affect calculations"?

sambaxter commented 1 year ago

How about "Show/hide variants that do not impact calculations"?

On Wed, Jun 1, 2022 at 8:14 AM Nick Watts @.***> wrote:

I'm having a bit of trouble deciding what to label this option. "Show/hide filtered variants" doesn't really work since it's not hiding all filtered variants, only those that are filtered to AC 0. Maybe "Show/hide variants that do not affect calculations"?

— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/aggregate-frequency-calculator/issues/96#issuecomment-1143529841, or unsubscribe https://github.com/notifications/unsubscribe-auth/AESSQ2CD2GZ2PBST7ICBRLDVM5H3JANCNFSM5W5MLF7A . You are receiving this because you authored the thread.Message ID: @.*** .com>

--

Samantha Baxter, MS, CGC

Associate Director, Genetic and Genomic Data Sharing

Licensed Genetic Counselor

@. @.>*