Genetic

† Look for the files with the most recent date.

Please cite (1) below if you use Raw WGSA variant annotations, cite (1) and (2) below if you use parsed WGSA annotations. DCC representatives can be invited as co-authors if you use variant grouping files provided below.
Citations:

1. WGSA :Liu X, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs R, Klein RJ and Boerwinkle E. (2016) WGSA: an annotation pipeline for human genome sequencing studies. Journal of Medical Genetics 53:111-112
2. WGSAparsr: Heavner BD, Jain D. WGSAParsr. https://github.com/UW-GAC/wgsaparsr/

‡ Look for the files with the most recent version.

WGS Read alignment data/CRAMs

A limited number of TOPMed Phase 1 CRAMs aligned to build 37 are available directly through the dbGaP Sequence Read Archive (SRA). These are accessible via their corresponding TOPMed accessions with dbGaP approval. All other CRAMs, including build 38 alignments for all TOPMed WGS samples, are hosted in NHLBI cloud buckets and accessed using the “Fusera” software.

Instructions for controlled access to TOPMed sequence data on the cloud 

Further documentation on dbGaP cloud access

A mapping of TOPMed NWD IDs to SRR IDs for build 38-aligned CRAMs is available on the exchange area: Combined_Study_Data/SRA_ID_mapping/
Files are listed by date and may not reflect all CRAMs available after the listed date. 

Variant Summary Data

The following repositories contain variant summary information for TOPMed studies that granted explicit permission. These resources are publicly available.

• BioData Catalyst TOPMed Imputation Server
• BRAVO (Browse All Variants Online) Variant Browser
• dbSNP (Database of Single Nucleotide Polymorphisms)
• Genomic Summary Results
• gnomAD (Genome Aggregation Database

Imputation Reference Panel and Server

A TOPMed reference panel and imputation server is available through NHLBI BioData Catalyst®. The resource is available to the scientific community at https://imputation.biodatacatalyst.nhlbi.nih.gov/.