Hi all, wanted to make folks aware of a new resource that is now available to aid those working with Fox Insight Genetic Sub-study (FIGS) data.
If you visit the Fox DEN > Resources page [link], we have made available additional documentation on genotyping procedures and QC methods for these data within the Genetic Sub-study documentation download: [link].
Huge thanks to @mattk for leading the authorship of this and to @hamptonl for providing additional review.
Thank you @jgottesman! One thing to note for FIGS users, we are in the process of updating the platform versions table (Genetic > platform_versions) that coincides with this updated documentation. Stay tuned!
Hi all, following up on this thread to note that the platform_versional variable’s values have been updated in Fox DEN. These new values (which can be found in the Genetics table) help to ensure alignment with expected call rates by plaform (as detailed in the FIGS documentation).
This change addresses the fact that sub-study participants may have been genotyped on multiple platforms. In such cases, the genotypes for SNPs across the platforms were merged together and are indicated by a “+” in the platform version data (Genetic > Platform Version). For example, a participant genotyped on both V2 and V5 is represented as “ILMN_GSA_CUSTOMv5+ILMN_550Qv1_CUSTOMv2”. For SNPs present on multiple platforms, the genotype for the most recent platform was used.
Thanks to @mattk@hamptonl and @mike for helping us continue to improve data quality.