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Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering

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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nature08494openalex-snapshot
Finding the missing heritability of complex diseases
inferredcites →https://doi.org/10.1038/nature11632openalex-snapshot
An integrated map of genetic variation from 1,092 human genomes
inferredcites →https://doi.org/10.1038/nature11690openalex-snapshot
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
inferredcites →https://doi.org/10.1038/nbt.2198openalex-snapshot
Performance comparison of benchtop high-throughput sequencing platforms
inferredcites →https://doi.org/10.1038/nbt.2522openalex-snapshot
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inferredcites →https://doi.org/10.1038/ng.2770openalex-snapshot
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
inferredcites →https://doi.org/10.1038/ng.610openalex-snapshot
Estimation of effect size distribution from genome-wide association studies and implications for future discoveries
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/ng.952openalex-snapshot
Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease
inferredcites →https://doi.org/10.1038/nrg3502openalex-snapshot
Genetic insights into common pathways and complex relationships among immune-mediated diseases
inferredcites →https://doi.org/10.1038/nrg3803openalex-snapshot
Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq214openalex-snapshot
A statistical method for the detection of variants from next-generation resequencing of DNA pools
inferredcites →https://doi.org/10.1093/bioinformatics/btu356openalex-snapshot
Toward better understanding of artifacts in variant calling from high-coverage samples
inferredcites →https://doi.org/10.1093/nar/gkq603openalex-snapshot
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
inferredcites →https://doi.org/10.1111/j.1399-0004.2010.01535.xopenalex-snapshot
Evolutionary evidence of the effect of rare variants on disease etiology
inferredcites →https://doi.org/10.1111/mec.12360openalex-snapshot
Estimation of population allele frequencies from next‐generation sequencing data: pool‐versus individual‐based genotyping
inferredcites →https://doi.org/10.1126/science.1217876openalex-snapshot
An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People
inferredcites →https://doi.org/10.1126/science.1219240openalex-snapshot
Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes
inferredcites →https://doi.org/10.1186/1471-2105-15-125openalex-snapshot
Effective filtering strategies to improve data quality from population-based whole exome sequencing studies
inferredcites →https://doi.org/10.1186/ar3204openalex-snapshot
Promise and pitfalls of the Immunochip
inferredcites →https://doi.org/10.1371/journal.pone.0018353openalex-snapshot
Efficient and Cost Effective Population Resequencing by Pooling and In-Solution Hybridization
inferredcites →https://doi.org/10.1371/journal.pone.0080422openalex-snapshot
Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species
inferredcites →https://doi.org/10.1534/genetics.110.114397openalex-snapshot
The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples
inferredcites →https://doi.org/10.1534/genetics.110.121012openalex-snapshot
To Pool, or Not to Pool?

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Additional file 1 of High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing
inferred← citeshttps://doi.org/10.6084/m9.figshare.19395961openalex-snapshot
Additional file 2 of High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing
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inferred← citeshttps://doi.org/10.7287/peerj.10186v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10186v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.10186v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.10186openalex-snapshot
Genomics versus mtDNA for resolving stock structure in the silky shark ( Carcharhinus falciformis )
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