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Efficient genotype compression and analysis of large genetic variation datasets

https://doi.org/10.1101/018259
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What this work says

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

inferredcites →https://doi.org/10.1038/nature01140openalex-snapshot
Detecting recent positive selection in the human genome from haplotype structure
inferredcites →https://doi.org/10.1038/nature06250openalex-snapshot
Genome-wide detection and characterization of positive selection in human populations
inferredcites →https://doi.org/10.1038/nature11632openalex-snapshot
An integrated map of genetic variation from 1,092 human genomes
inferredcites →https://doi.org/10.1046/j.1529-8817.2003.00060.xopenalex-snapshot
The evolution and population genetics of theALDH2locus: random genetic drift, selection, and low levels of recombination
inferredcites →https://doi.org/10.1073/pnas.1322563111openalex-snapshot
Searching for missing heritability: Designing rare variant association studies
inferredcites →https://doi.org/10.1086/519795openalex-snapshot
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btq671openalex-snapshot
Tabix: fast retrieval of sequence features from generic TAB-delimited files
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/btu014openalex-snapshot
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
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/10.1101/gr.083634.108openalex-snapshot
Fast and flexible simulation of DNA sequence data
inferredcites →https://doi.org/10.1101/gr.114819.110openalex-snapshot
Efficient storage of high throughput DNA sequencing data using reference-based compression
inferredcites →https://doi.org/10.1101/gr.8.3.175openalex-snapshot
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
inferredcites →https://doi.org/10.1101/gr.8.3.186openalex-snapshot
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
inferredcites →https://doi.org/10.1109/ssdm.2002.1029710openalex-snapshot
Compressing bitmap indexes for faster search operations
inferredcites →https://doi.org/10.1111/j.1558-5646.1984.tb05657.xopenalex-snapshot
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
inferredcites →https://doi.org/10.1126/science.1217283openalex-snapshot
Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants
inferredcites →https://doi.org/10.1371/journal.pbio.0040072openalex-snapshot
A Map of Recent Positive Selection in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1001322openalex-snapshot
Testing for an Unusual Distribution of Rare Variants

What points at this work

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

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa1004openalex-snapshot
Sparse Project VCF: efficient encoding of population genotype matrices
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv613openalex-snapshot
BGT: efficient and flexible genotype query across many samples
inferred← citeshttps://doi.org/10.1101/043430openalex-snapshot
Computational Pan-Genomics: Status, Promises and Challenges
inferred← citeshttps://doi.org/10.1101/gr.247965.118openalex-snapshot
Pedigree-based estimation of human mobile element retrotransposition rates
inferred← citeshttps://doi.org/10.1186/s12859-019-2698-4openalex-snapshot
JOA: Joint Overlap Analysis of multiple genomic interval sets
inferred← citeshttps://doi.org/10.1186/s13059-016-0973-5openalex-snapshot
Vcfanno: fast, flexible annotation of genetic variants
inferred← citeshttps://doi.org/10.21203/rs.3.rs-944936/v1openalex-snapshot
Compression with unified and accessible byte blocks to enhance management and analyses of UKBB-scale genotypes
inferred← citeshttps://doi.org/10.7287/peerj.preprints.1426v1openalex-snapshot
Tiling the genome into consistently named subsequences enables precision medicine and machine learning with millions of complex individual data-sets
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