Hello,
Thanks for sharing this valuable resource (https://www.synapse.org/#!Synapse:syn25672239).
Would you like to share the genotype data?
Best
Created by Benxia Hu BXH Here is a [query showing all the vcf files from the MSBB WGS data ](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063.28%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22study%22%2C%22facetValues%22%3A%5B%22MSBB%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22assay%22%2C%22facetValues%22%3A%5B%22wholeGenomeSeq%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22fileFormat%22%2C%22facetValues%22%3A%5B%22vcf%22%5D%7D%5D%7D)-- you can see the MSBB WGS methods description on the "Study Details" page to see the breakdown of the various files, but there is one set of files describing variants (with and without annotation) across all individuals in the study per chromosome. The chromosome is indicated by the last number after the "date_" and before the ".recalibrated" in the filenames.
Is that what you are looking for? thanks for porviding those useful infomation. I just check MSBB. However, MSBB has not provided comprehensive vcf file explaining genotype of each individual. Hi there, the individuals from the SuperAgerEpiMap study are part of the [Mt Sinai Brain Bank (MSBB) study](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn3159438) in the AD Knowledge Portal. You can identify which individuals from this study were part of the SuperAgerEpiMap study via the individualIDs in the biospecimen metadata file (syn25724246), and then find the WGS files associated with those individuals from the MSBB study.
Let me know if you have any other questions!
Abby