Open-source mapping and variant calling for large-scale NGS data from original base-quality scores

Krasheninina, Olga; Hwang, Yi‐Ting; X, Bai; Zalcman, Adam; Maxwell, Evan K.; Jg, Reid; Wj, Salerno

doi:10.1101/2020.12.15.356360

Cited by 9 publications

(3 citation statements)

References 16 publications

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“…The OQFE protocol retains all reads and original quality scores such that the original FASTQ is completely recoverable from the resulting CRAM file. Single-sample variants are called with DeepVariant v0.10.0 54 using default WGS parameters or custom exome parameters 53 , generating a gVCF for each input OQFE CRAM file. These gVCFs are aggregated and joint-genotyped with GLnexus v1.3.1.…”

Section: Methodsmentioning

confidence: 99%

“…Variant calling. The MCPS WES and WGS data were reference-aligned with the OQFE protocol 53 which employs BWA MEM to map all reads to the GRCh38 reference in an alt-aware manner, marks read duplicates, and adds additional per-read tags. The OQFE protocol retains all reads and original quality scores such that the original FASTQ is completely recoverable from the resulting CRAM file.…”

Section: Blood Sample Collection Processing and Storage And Dna Extra...mentioning

confidence: 99%

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Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study

Ziyatdinov

Torres

Alegre-Díaz

et al. 2022

Preprint

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The Mexico City Prospective Study (MCPS) is a prospective cohort of over 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City. We generated genotype and exome sequencing data for all individuals, and whole genome sequencing for 10,000 selected individuals. We uncovered high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Native American, European and African ancestry, with extensive admixture from indigenous groups in Central, Southern and South Eastern Mexico. Native Mexican segments of the genome had lower levels of coding variation, but an excess of homozygous loss of function variants compared with segments of African and European origin. We estimated population specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Native Mexico at exome variants, all available via a public browser. Using whole genome sequencing, we developed an imputation reference panel which outperforms existing panels at common variants in individuals with high proportions of Central, South and South Eastern Native Mexican ancestry. Our work illustrates the value of genetic studies in populations with diverse ancestry and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States where the Hispanic/Latino population is predominantly of Mexican descent.

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Section: Methodsmentioning

confidence: 99%

Section: Blood Sample Collection Processing and Storage And Dna Extra...mentioning

confidence: 99%

Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study

Ziyatdinov

Torres

Alegre-Díaz

et al. 2022

Preprint

Self Cite

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show abstract

“…This study was conducted with whole-exome sequencing data from 454,797 participants in the UK Biobank cohort, for which variants were retrieved from the OQFE version [63] of the whole-exome VCF files (field ID: 23148). The transfer of human data was approved and overseen by The UK Biobank Ethics Advisory Committee (Project ID [PID]: 51135).…”

Section: Methodsmentioning

confidence: 99%

Empowering rare variant burden-based gene-trait association studies via optimized computational predictor choice

Kuang

et al. 2021

Preprint

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Computational predictors can help interpret pathogenicity of human genetic variants, especially for the majority of variants where no experimental data are available. However, because we lack a high-quality unbiased test set, identifying the best-performing predictors remains a challenge. To address this issue, we evaluated missense variant effect predictors using genotypes and traits from a prospective cohort. We considered 139 gene-trait combinations with rare-variant burden association based on at least one of four systematic studies using phenotypes and whole-exome sequences from ~200K UK Biobank participants. Using an evaluation set of 35,525 rare missense variants and the relevant associated traits, we assessed the correlation of participants' traits with scores derived from 20 computational variant effect predictors. We found that two predictors—VARITY and REVEL—outperformed all others according to multiple performance measures. We expect that this study will help in selecting variant effect predictors, for both research and clinical purposes, while providing an unbiased benchmarking strategy that can be applied to additional cohorts and predictors.

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Exome-wide screening identifies novel rare risk variants for bone mineral density

Pan

Zhao

et al. 2023

Osteoporos Int

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Open-source mapping and variant calling for large-scale NGS data from original base-quality scores

Cited by 9 publications

References 16 publications

Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study

Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study

Empowering rare variant burden-based gene-trait association studies via optimized computational predictor choice

Exome-wide screening identifies novel rare risk variants for bone mineral density

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