Syzygy protocols

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Syzygy statistics

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Syzygy specifications


Unique identifier OMICS_02166
Name Syzygy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
License MIT License
Computer skills Advanced
Version 1.2.7
Stability Stable
Maintained Yes



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  • person_outline Mark Daly <>
  • person_outline Syzygy Team <>

Publication for Syzygy

Syzygy in pipelines

PMCID: 4363375
PMID: 25781923
DOI: 10.1371/journal.pgen.1004925

[…] lane of flow-cell on an illumina hiseq 2000 (illumina inc, sandiego, ca, sequences were aligned against human reference sequence (37d5) using stampy [] and variants called by the syzygy (1.2.6) algorithm to create a vcf file. syzygy implements a bayes likelihood calculation to allow a base calling strategy that is particularly suited to the calling of variants in pooled […]

PMCID: 3610211
PMID: 23514105
DOI: 10.1186/2040-2392-4-5

[…] gene exons within the libraries. 76 bp reads were aligned to the genome using novoalign (novocraft, selangor, malaysia) and mutation analysis was performed with the genome analysis toolkit [,] and syzygy []., confirmation of the potentially deleterious variants identified was performed by sanger sequencing on an abi 3730 capillary sequencer and dna sequence analysis was performed using […]

PMCID: 3772057
PMID: 24068945
DOI: 10.1371/journal.pgen.1003723

[…] were aligned to the genome using maq algorithm and base qualities were recalibrated using gatk (genome analysis toolkit) . finally, variant discovery was performed using the previously described syzygy software, designed to analyze sequencing data from pooled dna sequencing ., we randomly selected 237 high quality variants for validation in our 350 discovery dnas samples using sequenom […]

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Syzygy in publications

PMCID: 5645406
PMID: 29042551
DOI: 10.1038/s41467-017-00831-x

[…] by illumina gaii or illumina hiseq2000. sequencing reads were aligned and processed by picard analysis pipeline ( variants and afs were called using syzygy and snver. we used annovar to annotate variants for refseq genes (hg19), gerp scores, encode dhs cluster, and 1000 g data., snp genotyping was performed using the sequenom massarray iplex […]

PMCID: 5256917
PMID: 28114305
DOI: 10.1371/journal.pone.0170222

[…] the average coverage per individual was 30x., in order to distinguish true calls from sequencing error, three different calling algorithms specific for pooled data were used (vipr [], snver [] and syzygy []). vipr was less sensitive than the other two algorithms and it called a much smaller number of variants, 39,211 snps and 459 deletions, compared to 62,506 snps and 5,811 indels by snver […]

PMCID: 4452458
PMID: 25450229
DOI: 10.1038/mp.2014.156

[…] bp paired-end) according to the protocols suggested by the manufacturers. base quality recalibration and alignment were performed using the burrows-wheeler aligner (bwa) referencing hg19. we used syzygy to call variants from the pooled targeted resequencing data., together, about 62 gb (868 million reads) of raw sequencing data was obtained from deep-sequencing analysis of the eight pooled […]

PMCID: 3784764
PMID: 24002087
DOI: 10.1038/tp.2013.75

[…] realignment around potential insertion/deletions (indels) and base quality score recalibration were performed before variant calling. for single-nucleotide polymorphism (snp) calling, we used syzygy, an algorithm specifically designed to call bases in pooled samples., for each snp, analysis by seattleseq ( provided information […]

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Syzygy institution(s)
Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Universite de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
Syzygy funding source(s)
Supported by NHGRI Sequencing Grant, and DK 83756, Funds from the Helmsley Trust, National Institutes of Health Grants AI062773, DK060049 and DK043351, fellowships from La Fondation pour la Recherche Medicale and the Crohn’s and Colitis Foundation of America, grants from the U.S. National Institutes of Allergy and Infectious Diseases (AI065687; AI067152) from the U.S. National Institute of Diabetes and Digestive and Kidney Diseases (DK064869; DK062432), the Crohn’s and Colitis Foundation of America (SRA512), la Fondation de l’institut de cardiologie de Montréal, the Crohn’s and Colitis Foundation of Canada (CCFC), the Fonds de Recherche en Santé du Québec, and the Canadian Institutes of Health Research, the Italian Ministry for Health GR-2008-1144485 and unrestricted research grant of Giuliani spa, with case collections provided by the Italian Group for IBD (IG-IBD), grants: DK062431, DK062422, DK062420, DK062432, DK062423, DK062413, and DK062429, NCRR grant M01-RR00425 to the Cedars-Sinai General Research Center Genotyping core U01-DK062413(IBD GRC), P01-DK046763 (IBD PPG), Southern California Diabetes Endocrinology Research Center grant, DK063491, R21-DK84554-01, and U01 DK062413, the German Ministry of Education and Research through the National Genome Research Network (NGFN), the Swedish Research Council, the Bengt Ihre’s Foundation, and the Örebro University Hospital Research foundation.

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