An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data (Q34538741)

2 August 2017

title

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data (English)

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2 August 2017

Jin Yu

3

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Richard A Gibbs

series ordinal

4

object named as

Richard A Gibbs

1 reference

2 August 2017

Yi Wang

1

1 reference

2 August 2017

James Lu

series ordinal

2

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2 August 2017

Fuli Yu

series ordinal

5

1 reference

2 August 2017

publication date

7 January 2013

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2 August 2017

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2 August 2017

volume

23

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2 August 2017

issue

5

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2 August 2017

page(s)

833-842

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

2 August 2017

cites work

1 reference

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Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms

7 July 2018

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A linear complexity phasing method for thousands of genomes

7 July 2018

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

7 July 2018

1 reference

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Comparison of sequence reads obtained from three next-generation sequencing platforms

7 July 2018

1 reference

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Genotype and SNP calling from next-generation sequencing data

7 July 2018

1 reference

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

7 July 2018

1 reference

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Low-coverage sequencing: implications for design of complex trait association studies

7 July 2018

1 reference

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Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads

7 July 2018

1 reference

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Improving SNP discovery by base alignment quality

7 July 2018

1 reference

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Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

7 July 2018

1 reference

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MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

7 July 2018

1 reference

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A map of human genome variation from population-scale sequencing

7 July 2018

1 reference

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SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

7 July 2018

1 reference

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Dindel: accurate indel calls from short-read data

7 July 2018

1 reference

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

7 July 2018

1 reference

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BFAST: an alignment tool for large scale genome resequencing

7 July 2018

1 reference

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Human triallelic sites: evidence for a new mutational mechanism?

7 July 2018

1 reference

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VarScan: variant detection in massively parallel sequencing of individual and pooled samples

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

The Sequence Alignment/Map format and SAMtools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Fast and accurate short read alignment with Burrows-Wheeler transform

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Evaluation of next generation sequencing platforms for population targeted sequencing studies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Population genomics of domestic and wild yeasts

7 July 2018

1 reference

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Shape-IT: new rapid and accurate algorithm for haplotype inference

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Next-generation DNA sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Mapping short DNA sequencing reads and calling variants using mapping quality scores

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

A comparison of phasing algorithms for trios and unrelated individuals

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

A haplotype map of the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Haplotype and missing data inference in nuclear families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

SSAHA: a fast search method for large DNA databases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

Model-based inference of haplotype block variation.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3638139

TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA.

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23296920

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.146084.112

1 reference

2 August 2017

1 reference

2 August 2017

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