We are analyzing https://link.springer.com/article/10.1186/s12859-014-0356-4.

Title:
ANGSD: Analysis of Next Generation Sequencing Data | BMC Bioinformatics
Description:
Background High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. Results We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. Conclusions The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.
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Keywords {🔍}

data, angsd, genotype, pubmed, article, analyses, sequencing, file, allele, figure, frequency, google, scholar, analysis, methods, based, samtools, gatk, central, population, cas, snp, sample, calling, likelihood, additional, model, information, genotypes, sites, site, samples, genome, quality, estimated, authors, likelihoods, bioinformatics, albrechtsen, error, individuals, nature, baq, nielsen, program, gls, estimation, table, original, called,

Topics {✒️}

/nature/journal/v467/n7319/full/nature09534 article download pdf reduces false-positive associations genome-wide association studies thorfinn sand korneliussen /goldenpath/hg19/multiz46way/maf accurate genotype/haplotype inference high-coverage genome sequence abba-baba/d-statistic [18] abba-baba d-statistic [18] site-wise association testing centromeric/telomeric regions defined low-coverage sequencing data performing association studies privacy choices/manage cookies estimating inbreeding coefficients short dna sequences joint frequency spectrum association studies based genetic informational network genomic start position bcf/vcf files open access license joint allele frequency genotype likelihoods input open source mutithreaded population genetic inferences proper simulation study sample allele frequency site frequency spectrum site-frequency spectrum assuming realistic recombination authors’ original file abba-baba test medium coverage data association mapping utilizing project home page population genetic analyses article korneliussen high call rates generation sequencing data generation sequencing data short read alignment sequencing error rates population allele frequency multiz46way dataset sync table 3 d-stat raw sequencing files genotype likelihood model population-scale sequencing

Schema {🗺️}

WebPage:
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         headline:ANGSD: Analysis of Next Generation Sequencing Data
         description:High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.
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         dateModified:2014-11-25T00:00:00Z
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            Bioinformatics
            Population genetics
            Association studies
            Microarrays
            Computational Biology/Bioinformatics
            Computer Appl. in Life Sciences
            Algorithms
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      headline:ANGSD: Analysis of Next Generation Sequencing Data
      description:High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.
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         Bioinformatics
         Population genetics
         Association studies
         Microarrays
         Computational Biology/Bioinformatics
         Computer Appl. in Life Sciences
         Algorithms
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      name:Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
      name:Department of Integrative Biology and Statistics, UC-Berkeley, Berkeley, USA

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