Change in VariantID filter in Cohort Browser in RAP
Hi,
I am using the cohort browser tool to identify individuals who has P/LP variants.
1)I wanted to know if there is any change in RAP platform in terms of data or output displayed in cohort browser.
Details-I had filtered 36 GATA2 P/LP variants using Cohort Browser 1 year back. That time i had 25 individuals with one of the 36 variant. But now as of November,2025. when i used the same variant list. I am just getting 5 individual?
Could this be because it only shows germline variants now?
2)Which data was accessed before when the “VariantID” filter is used? Is it WES data,WGS data or Genotype data?
Please let me know! And any suggestions to do it more efficiently is welcome. Right now its very manual and repitative.
Thank you for help!
Comments
4 comments
Hi Ashwin,
the genomic tool within the UKB-RAP cohort browser is definitely using the WES data, and has always been using the WES data.
So far as I know, it is only using germline variants, and so far as I know it has always been using only germline variants.
I don't know whether the annotation might have been updated. Does anyone else know?
This may be a result of participant withdrawals.
Thank you for the response! I double checked if the participants which i previously had in my GATA2 Cases have withdrawn but it looks like they are still part of the study. I cross-checked with the list of participant ids which UKB team sends when participants withdraw.
Also i can see the participants come up when i search them via cohort browser.
Hi Ashwin, have you definitely used the same filter? For example, if you selected “Any Zygosity” last year but “Homozygous” this year you would get fewer results. The selection of the assay, the type and the effects could also change the resulting list.
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