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Literature DB >> 26550772

Efficient genotype compression and analysis of large genetic-variation data sets.

Ryan M Layer¹, Neil Kindlon¹, Konrad J Karczewski², Aaron R Quinlan^1,3,4.

Abstract

Genotype Query Tools (GQT) is an indexing strategy that expedites analyses of genome-variation data sets in Variant Call Format based on sample genotypes, phenotypes and relationships. GQT's compressed genotype index minimizes decompression for analysis, and its performance relative to that of existing methods improves with cohort size. We show substantial (up to 443-fold) gains in performance over existing methods and demonstrate GQT's utility for exploring massive data sets involving thousands to millions of genomes. GQT can be accessed at https://github.com/ryanlayer/gqt.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2015 PMID： 26550772 PMCID： PMC4697868 DOI： 10.1038/nmeth.3654

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

7 in total

1. Fast and flexible simulation of DNA sequence data.

Authors: Gary K Chen; Paul Marjoram; Jeffrey D Wall
Journal: Genome Res Date: 2008-11-24 Impact factor: 9.043

2. Searching for missing heritability: designing rare variant association studies.

Authors: Or Zuk; Stephen F Schaffner; Kaitlin Samocha; Ron Do; Eliana Hechter; Sekar Kathiresan; Mark J Daly; Benjamin M Neale; Shamil R Sunyaev; Eric S Lander
Journal: Proc Natl Acad Sci U S A Date: 2014-01-17 Impact factor: 11.205

3. BEDTools: a flexible suite of utilities for comparing genomic features.

Authors: Aaron R Quinlan; Ira M Hall
Journal: Bioinformatics Date: 2010-01-28 Impact factor: 6.937

4. Recent explosive human population growth has resulted in an excess of rare genetic variants.

Authors: Alon Keinan; Andrew G Clark
Journal: Science Date: 2012-05-11 Impact factor: 47.728

5. The variant call format and VCFtools.

Authors: Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A Albers; Eric Banks; Mark A DePristo; Robert E Handsaker; Gerton Lunter; Gabor T Marth; Stephen T Sherry; Gilean McVean; Richard Durbin
Journal: Bioinformatics Date: 2011-06-07 Impact factor: 6.937

6. Big Data: Astronomical or Genomical?

Authors: Zachary D Stephens; Skylar Y Lee; Faraz Faghri; Roy H Campbell; Chengxiang Zhai; Miles J Efron; Ravishankar Iyer; Michael C Schatz; Saurabh Sinha; Gene E Robinson
Journal: PLoS Biol Date: 2015-07-07 Impact factor: 8.029

7. An integrated map of genetic variation from 1,092 human genomes.

Authors: Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal: Nature Date: 2012-11-01 Impact factor: 49.962

7 in total

25 in total

1. Accurate, scalable cohort variant calls using DeepVariant and GLnexus.

Authors: Taedong Yun; Helen Li; Pi-Chuan Chang; Michael F Lin; Andrew Carroll; Cory Y McLean
Journal: Bioinformatics Date: 2021-01-05 Impact factor: 6.937

2. Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework.

Authors: Miaoxin Li; Jiang Li; Mulin Jun Li; Zhicheng Pan; Jacob Shujui Hsu; Dajiang J Liu; Xiaowei Zhan; Junwen Wang; Youqiang Song; Pak Chung Sham
Journal: Nucleic Acids Res Date: 2017-05-19 Impact factor: 16.971

Efficient genotype compression and analysis of large genetic-variation data sets.

1. Fast and flexible simulation of DNA sequence data.

2. Searching for missing heritability: designing rare variant association studies.

3. BEDTools: a flexible suite of utilities for comparing genomic features.

4. Recent explosive human population growth has resulted in an excess of rare genetic variants.

5. The variant call format and VCFtools.

6. Big Data: Astronomical or Genomical?

7. An integrated map of genetic variation from 1,092 human genomes.

1. Accurate, scalable cohort variant calls using DeepVariant and GLnexus.

2. Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework.

3. SeqArray-a storage-efficient high-performance data format for WGS variant calls.

Review 4. Advances in Genomic Discovery and Implications for Personalized Prevention and Medicine: Estonia as Example.

5. Sparse Allele Vectors and the Savvy Software Suite.

Review 6. Computational pan-genomics: status, promises and challenges.

Review 7. Novel bioinformatic developments for exome sequencing.

8. Vcfanno: fast, flexible annotation of genetic variants.

9. Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.

10. Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints.