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WES/WGS SNV VCFs and Indel genotypes released

This seventh ADSP data release on April 12, 2016 includes:

(1) WES and WGS SNV VCF files

(2) WES and WGS Indel PLINK files

Please use the release notes provided by dbGaP to obtain detailed information about study release updates.

    ADSP Data Available through dbGaP:

      ADSP - Whole Genome Sequencing ADSP - Whole Exome Sequencing Comments
    DNA-Seq (BAM) n=578 n=10913 Sequence data available (plus n=38 replications w/out genotype data)
    Concordant SNV Genotypes (PLINK format) N/A n=10913 QC'ed genotypes that are concordant between the Atlas (Baylor's) and GATK (Broad's) calling pipelines (a subset of the consensus genotype set)
    Consensus Genotypes (PLINK and VCF format) n=578 n=10913 QC'ed genotypes that are concordant between Atlas and GATK pipelines as well as those that that were called uniquely by Atlas or GATK
    Concordant Indel Genotypes (PLINK format) n=578 n=10913 QC'ed genotypes that are concordant between the Atlas and GATK calling pipelines
    Phenotype Data n=4735 n=10913 Data of n=53 phenotype variables available (plus administrative data), including APOE genotype. WGS phenotypes include data of connecting family members.

    Past Data Releases:

    • The first ADSP data release occurred on November 25, 2013. It included the whole-genome sequencing data in BAM file format on 410 individuals.
    • The second ADSP data release occurred on March 31, 2014, and included the whole-genome sequencing data in BAM file format for an additional 168 individuals.
    • The third ADSP data release occurred on November 03, 2014 and included whole-exome sequencing data in BAM file format for 10,939 individuals.
    • The fourth ADSP data release occurred on February 13, 2015 and included revised ethnic data for subjects with whole-exome sequencing data.
    • The fifth ADSP data release occurred on July 13, 2015 and included whole-genome genotypes and updated phenotypes as well as changes to pedigree structures and sample IDs.
    • The sixth ADSP data release occurred on December 8, 2015, and included whole-exome genotypes and updated phenotypes as well as changes to subject IDs.

    The ADSP data portal provides a customized interface for users to quickly identify and retrieve files by covariates, phenotypes, and data properties such as sequencing facility or coverage.

    Posted Date: 
    Thursday, April 28, 2016 - 13:15

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