Syzygy statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Syzygy

Tool usage distribution map

This map represents all the scientific publications referring to Syzygy per scientific context
info info

Associated diseases

This word cloud represents Syzygy usage per disease context

Popular tool citations

chevron_left SNP detection SNP detection Indel detection Population genetic analysis Indel detection chevron_right
Want to access the full stats & trends on this tool?


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




No version available



  • person_outline Mark Daly
  • person_outline Syzygy Team

Publication for Syzygy

Syzygy citations


Integrating evolutionary and regulatory information with a multispecies approach implicates genes and pathways in obsessive compulsive disorder

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

[…] sequenced 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. […]


Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment

PLoS Genet
PMCID: 4363375
PMID: 25781923
DOI: 10.1371/journal.pgen.1004925
call_split See protocol

[…] e 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 sample […]


Frequency of Rare Allelic Variation in Candidate Genes among Individuals with Low and High Urinary Calcium Excretion

PLoS One
PMCID: 3753300
PMID: 23991001
DOI: 10.1371/journal.pone.0071885

[…] Utilizing the Syzygy software , we compared all identified single nucleotide variants (SNVs) with three publically available SNP databases including dbSNP (, 1000 Genome Pr […]


Population based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

BMC Genomics
PMCID: 3534616
PMID: 23216810
DOI: 10.1186/1471-2164-13-683

[…] ation capture outperformed PCR or array-based hybridization methods and report a sensitivity and specificity of 98.2% and 97.0% for a smaller pool of 20 individuals using MAQ v0.1.7 for alignment and Syzygy for SNV calling with no analysis of INDELs. Bansal and colleagues surveyed 594 kb in pools of 20 and report a sensitivity of 93% at 30-fold coverage for substitutions and a positive predictive […]


An Evaluation of Different Target Enrichment Methods in Pooled Sequencing Designs for Complex Disease Association Studies

PLoS One
PMCID: 3206031
PMID: 22069447
DOI: 10.1371/journal.pone.0026279

[…] The sensitivity, specificity and frequency estimation analyses were conducted by comparing the variants and frequency estimates from the Syzygy calls to the known variant content in the pool using existing genotype data for each pooled individual. We used the non-redundant release 27 HapMap genotypes for the 31 HapMap individuals used […]


A rare penetrant mutation in CFH confers high risk of age related macular degeneration

Nat Genet
PMCID: 3225644
PMID: 22019782
DOI: 10.1038/ng.976

[…] it (GATK). We called SNP genotypes with the Unified Genotyper module in GATK based on three metrics a) mapping quality score b) coverage and c) strand bias (see Low coverage samples (<10x depth for >20kb) and samples with >15% genotype error with 19 SNPs genotyped on the Affymetrix array were removed. For this study we required that the minimum mapp […]

Want to access the full list of citations?
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.

Syzygy reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Syzygy