Dataset Information

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.

ABSTRACT: The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed "consensus calling," to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.

SUBMITTER: Naj AC

PROVIDER: S-EPMC6397097 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.

Naj Adam C AC Lin Honghuang H Vardarajan Badri N BN White Simon S Lancour Daniel D Ma Yiyi Y Schmidt Michael M Sun Fangui F Butkiewicz Mariusz M Bush William S WS Kunkle Brian W BW Malamon John J Amin Najaf N Choi Seung Hoan SH Hamilton-Nelson Kara L KL van der Lee Sven J SJ Gupta Namrata N Koboldt Daniel C DC Saad Mohamad M Wang Bowen B Nato Alejandro Q AQ Sohi Harkirat K HK Kuzma Amanda A Wang Li-San LS Cupples L Adrienne LA van Duijn Cornelia C Seshadri Sudha S Schellenberg Gerard D GD Boerwinkle Eric E Bis Joshua C JC Dupuis Josée J Salerno William J WJ Wijsman Ellen M EM Martin Eden R ER DeStefano Anita L AL

Genomics 20180529 4

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel prot ...[more]

PMID: 29857119

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Dataset Information

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.

Publications

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.

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