Sequencing Pipelines

 

 

Sequencing for the Discovery and Extension Phases was conducted by three Large Scale Sequencing/Analysis Centers (LSACs): 1) the Human Genome Sequencing Center at Baylor College of Medicine, 2) Broad Institute, and 3) Genome Institute at Washington University.  The three LSACs generated paired-end sequencing BAM files mapped to build 37 using the settings in the table below. Discovery phase data mapped to build 37 is available for request through dbGaP, phs000572. BAM files are collected together from dbGaP, then called as project-level VCFs by Broad Institute and Baylor College of Medicine (these are intermediate files and not available to the public).  The ADSP Quality Control Work Group combines the two project-level VCF datasets and performs QC and concordance checks into an overall ADSP VCF file.

 

The Genome Center for Alzheimer's Disease (GCAD) remapped all Discovery and Extension phase data to build 38 using the settings in the table below. The whole genome data are available for request through the NIAGADS Data Sharing Service (DSS). More information about the data available can be found on the DSS ADSP study page.  

 

The GCAD Quality Control team along with assistance from the ADSP Quality Control Work Group performs QC and concordance checks and generates a whole-genome project level VCF file.

 

 

 

Broad Institute used the Illumina Rapid Capture Exome (ICE) kit, download target regions.

Baylor and WashU used the Nimblegen's VCRome v2.1, download target regions.