Identify missing data on SNP on RAP

Marie-Anne Pietrowski

Hello,

I'm looking for a way to identify missing data when searching for one specific SNP in cohort browser. I don't see missing data as I see it for the phenotypic data, is it possible to find it directly on the cohort browser ?

Thank you

Comments

4 comments

Date Votes
  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Marie-Anne,

    the genetic data in the cohort browser comes from the Whole Exome Sequencing (WES), described in Category 170 .  To identify the participants that do not have any WES data, please use field 32050 Release tranche , where a NULL value in 32050 means “no WES data”.

    Thank you for using the forum.

    0
  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst
    • Edited

    Field 32050 should be within the cohort browser.   However, field 32050 was new in 2023.    If your UKB-RAP project is quite old, then it might not include field 32050.   To receive field 32050, please wait until data dispense is working again (see this announcement) and then create a new UKB-RAP project.

    0
  • Comment author
    Marie-Anne Pietrowski

    Thank you, I have access to field 32050, do you know what quality controls need to be performed on data from the WES please ?

    0
  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    I am not a geneticist, and I can't help with that question.    There are two publications that describe what qc has already been performed: by Van Hout et al and Backman et al .

    I suggest you start a new thread, with that question in the title, to see if other researchers are able to advise.

    0

Please sign in to leave a comment.