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genotyping human template

Template for Genotyping_Human [Download]

Attribute Description Required columnType DependsOn Source Parent Valid Values
adjustedCovariates Any covariates the GWAS is adjusted for. Multiple values can be listed separately by a semicolon (;). Example - age;sex False STRING ManifestColumn
arrayInformation Additional information about the genotyping array. For example, for targeted arrays, please provide the specific type of array. Example - Immunochip False STRING ManifestColumn
arrayManufacturer Manufacturer of the genotyping array used for the discovery stage. Separate multiple manufacturers by a semicolon (;). Example - Illumina, Affymetrix, Perlegen False STRING ManifestColumn
backgroundTrait Any background trait(s) shared by all individuals in the GWAS (e.g. in both cases and controls). Example - Nicotine dependence False STRING ManifestColumn
genotypeTechnology Method(s) used to genotype variants in the discovery stage. Separate multiple methods separated by a semicolon (;). Example - genome-wide genotyping array, exome-wide sequencing, targeted genotyping array True STRING ManifestColumn
imputation Were SNPs imputed for the discovery GWAS? True STRING ManifestColumn
imputationPanel Panel used for imputation. Example - 1000 Genomes Phase 3 False STRING ManifestColumn
imputationSoftware Imputation software. Example - IMPUTE False STRING ManifestColumn
measurementTechnique The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
numberIndividuals Number of individuals in a group. Example - 2000 True INTEGER ManifestColumn
readmeFile The name of any readme file uploaded to Synapse. Example - example.tsv False STRING ManifestColumn
reagentCatalogNumber If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'. False STRING ManifestColumn
reagentContact The contact information is particularly helpful when the reagent is not from a commercial vendor. False STRING ManifestColumn
reagentIDs One or more identifiers, separated by a semicolon (;). The reagent identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. False STRING ManifestColumn
reagentLotNumber The lot number is often provided by a reagent source when the reagent is replenished over time. False STRING ManifestColumn
reagentManufacturer The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g., collaborating labs). False STRING ManifestColumn
reagentName The reagent name is an alternative to the Reagent ID. False STRING ManifestColumn
reagentWeblink An internet address that may provide details of an assay reagent. False STRING ManifestColumn
reportedTrait The trait under investigation. Please describe the trait concisely but with enough detail to be clear to a non-specialist. Avoid the use of abbreviations; if these are necessary, please define them or their source in the readme file. Example - Reticulocyte count True STRING ManifestColumn
sampleType The type of sample collected or the term used to describe the source of a biospecimen used for a laboratory test. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
stage Stage of the experimental design. True STRING ManifestColumn Discovery,Not applicable,Not collected,Not specified,Other,Replication,Unknown
statisticalModel A brief description of the statistical model used to determine association significance. It is important to distinguish studies that would otherwise appear identical (e.g., the same trait analyzed using additive, dominant, and recessive models). Example - additive model False STRING ManifestColumn
summaryFile The name of any summary statistics file uploaded to Synapse. Example - example.tsv False STRING ManifestColumn
summaryStatisticsAssembly Genome assembly for the summary statistics. Example - GRCh38 False STRING ManifestColumn
treatmentAmountUnit Unit of treatment amount. False NUMBER ManifestColumn AFU,AI,AU/ml,DK units/ml,g/dl,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,other,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml
treatmentAmountValue The Amount Value indicates how much (concentration, mass, volume) of a treatment agent was applied to a sample. False STRING ManifestColumn
treatmentDurationUnit Unit of treatment duration. False STRING ManifestColumn d.p.c.,Days,Hours,Minutes,Months,Not applicable,Not collected,Not specified,Seconds,Unknown,Weeks,Years
treatmentDurationValue Duration of treatment. False NUMBER ManifestColumn
treatmentIDs One or more identifiers, separated by a semicolon (;). The treatment identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. False STRING ManifestColumn
treatmentName Treatments refer to in vitro modifications of samples. Three treatment types are supported- agent amount, duration, and temperature. The treatment name is an alternate identifier to the Treatment ID. False STRING ManifestColumn
treatmentTemperatureUnit Unit of treatment temperature. False STRING ManifestColumn C,F,K,Not specified
treatmentTemperatureValue Value of treatment temperature. False NUMBER ManifestColumn
useReadMeFile Was a readme file uploaded to Synapse? True STRING ManifestColumn
useReagent Was a reagent applied to the sample? True BOOLEAN ManifestColumn FALSE,TRUE
useSummaryFile Was a summary statitics file uploded to Synapse? True STRING ManifestColumn
useTreatment Was a treatment applied to the sample? True BOOLEAN ManifestColumn
variantCount The number of variants analysed in the discovery stage (after QC). Example - 52500 True STRING ManifestColumn
Component False
Filename False
specimenID Identifying string linked to a particular sample or specimen, provide by the data contributor True STRING sage.annotations-experimentalData.specimenID-0.0.2 ManifestColumn