eXclusionarY

Sun L, Wang Z, Lu T, Manolio TA, Paterson AD (2023). eXclusionarY: 10 years later, where are the sex chromosomes in GWASs?. The American Journal of Human Genetics, Volume 110, Issue 6, 903 - 912.

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This depository contains codes (and data) used for the analyses for the eXclusionarY commentary, including

Significant SNPs reported in the NHGRI-EBI GWAS catalog

Data is publicly available at https://www.ebi.ac.uk/gwas/docs/file-downloads; the specific download of the time-stamped dataset, GWASCatalog_allassoc_29Nov2022release.RData is included here.

Code used to perform the analysis is gwas_catalog_summary.R.

Genome-wide summary statistics reported in the NHGRI-EBI GWAS catalog

Data is publicly available at https://www.ebi.ac.uk/gwas/downloads/summary-statistics; the specific download of the time-stamped dataset is available at http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics.

Code used to perform the analysis is gwas_catalog_summary_stat_analysis.R.

The PolyGenic Score (PGS) catalog

Data is publicly available at https://www.pgscatalog.org/downloads; the specific download of the time-stamped dataset is available at http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores.

Code used to perform the analysis is pgs_catalog_analysis.R.

Heterogeneous analysis and reporting of the X chromosome in the NHGRI-EBI GWAS catalog

The catalog downloaded on 2020-03-08, gwas_catalog_v1.0.2-associations_e98_r2020-03-08.txt.zip, is included here.