Tutorial | University of Tartu Institute of Genomics

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Faculty of Arts and Humanities
Faculty phone: 
+372 737 5341
Faculty address: 
Jakobi 2, rooms 116–121, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5341
    Faculty address: 
    Jakobi 2, rooms 116–121, 51005 Tartu
  • Institute of History and Archaeology
    Faculty phone: 
    +372 737 5651
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Estonian and General Linguistics
    Faculty phone: 
    +372 737 5221
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Philosophy and Semiotics
    Faculty phone: 
    +372 737 5314
    Faculty address: 
    Jakobi 2, rooms 309–352, 51005 Tartu
  • Institute of Cultural Research
    Faculty phone: 
    (+372) 737 5223
    Faculty address: 
    Ülikooli 16, 51003 Tartu
  • School of Theology and Religious Studies
    Faculty phone: 
    +372 737 5301
    Faculty address: 
    Ülikooli 18–310, 50090 Tartu
  • College of Foreign Languages and Cultures
    Faculty address: 
    Lossi 3, 51003 Tartu
  • Viljandi Culture Academy
    Faculty phone: 
    +372 435 5232
    Faculty address: 
    Posti 1, 71004 Viljandi
Faculty of Social Sciences
Faculty phone: 
+372 737 5957
Faculty address: 
Lossi 36, 51003 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5900
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Institute of Education
    Faculty phone: 
    +372 737 6440
    Faculty address: 
    Salme 1a–29, 50103 Tartu
  • Johan Skytte Institute of Political Studies
    Faculty phone: 
    +372 737 5582
    Faculty address: 
    Lossi 36–301, 51003 Tartu
  • School of Economics and Business Administration
    Faculty phone: 
    +372 737 6310
    Faculty address: 
    J. Liivi 4, 50409 Tartu
  • Institute of Psychology
    Faculty phone: 
    +372 737 5902
    Faculty address: 
    Näituse 2, 50409 Tartu
  • School of Law
    Faculty phone: 
    +372 737 5390
    Faculty address: 
    Näituse 20–324, 50409 Tartu
  • Institute of Social Studies
    Faculty phone: 
    +372 737 5188
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Narva College
    Faculty phone: 
    +372 740 1900
    Faculty address: 
    Raekoja plats 2, 20307 Narva
  • Pärnu College
    Faculty phone: 
    +372 445 0520
    Faculty address: 
    Ringi 35, 80012 Pärnu
Faculty of Medicine
Faculty phone: 
+372 737 5326
Faculty address: 
Ravila 19, 50411 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5326
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Biomedicine and Translational Medicine
    Faculty phone: 
    +372 737 4210
    Faculty address: 
    Biomeedikum, Ravila 19, 50411 Tartu
  • Institute of Pharmacy
    Faculty phone: 
    +372 737 5286
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Dentistry
    Faculty phone: 
    +372 731 9856
    Faculty address: 
    Raekoja plats 6, 51003 Tartu
  • Institute of Clinical Medicine
    Faculty phone: 
    +372 737 5323
    Faculty address: 
    L. Puusepa 8, 50406 Tartu
  • Institute of Family Medicine and Public Health
    Faculty phone: 
    +372 737 4190
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Sport Sciences and Physiotherapy
    Faculty phone: 
    +372 737 5360
    Faculty address: 
    Jakobi 5–205, 51005 Tartu
Faculty of Science and Technology
Faculty phone: 
+372 737 5820
Faculty address: 
Vanemuise 46–208, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5820
    Faculty address: 
    Vanemuise 46–208, 51005 Tartu
  • Institute of Computer Science
    Faculty phone: 
    +372 737 5445
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Estonian Marine Institute
    Faculty phone: 
    +372 671 8902
    Faculty address: 
    Mäealuse 14, 12618 Tallinn
  • Institute of Physics
    Faculty address: 
    W. Ostwaldi 1, 50411 Tartu
  • Institute of Chemistry
    Faculty phone: 
    +372 737 5261
    Faculty address: 
    Ravila 14a, 50411 Tartu
  • Institute of Mathematics and Statistics
    Faculty phone: 
    +372 737 5860
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Institute of Molecular and Cell Biology
    Faculty phone: 
    +372 737 5011
    Faculty address: 
    Riia 23, 23b–134, 51010 Tartu
  • Tartu Observatory
    Faculty phone: 
    +372 737 4510
    Faculty address: 
    Observatooriumi 1, Tõravere, 61602 Tartumaa
  • Institute of Technology
    Faculty phone: 
    +372 737 4800
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Ecology and Earth Sciences
    Faculty phone: 
    +372 737 5835
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Institutions
  • Library
    Faculty phone: 
    +372 737 5702
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Youth Academy
    Faculty phone: 
    +372 737 5581
    Faculty address: 
    Uppsala 10, 51003 Tartu
  • Institute of Genomics
    Faculty phone: 
    +372 737 4000
    Faculty address: 
    Riia 23b, 51010 Tartu
  • Museum
    Faculty phone: 
    +372 737 5674
    Faculty address: 
    Lossi 25, 51003 Tartu
  • University of Tartu Natural History Museum and Botanical Garden
    Faculty phone: 
    +372 737 6076
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Support Units
  • Administrative Office
    Faculty phone: 
    +372 737 5606
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Centre for Entrepreneurship and Innovation
    Faculty phone: 
    +372 737 6339
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • University Office in Tallinn
    Faculty phone: 
    +372 737 6600
    Faculty address: 
    Teatri väljak 3, 10143 Tallinn
  • Estates Office
    Faculty phone: 
    +372 737 5137
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Finance Office
    Faculty phone: 
    +372 737 5125
    Faculty address: 
    Jakobi 4, 51005 Tartu
  • Grant Office
    Faculty phone: 
    +372 737 6215
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • Information Technology Office
    Faculty phone: 
    +372 737 6000, IT-help: +372 737 5500
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Human Resources Office
    Faculty phone: 
    +372 737 5145
    Faculty address: 
    Ülikooli 18, rooms 302 and 304, 50090 Tartu
  • Internal Audit Office
    Faculty address: 
    Ülikooli 17–103, 51005 Tartu
  • Marketing and Communication Office
    Faculty phone: 
    +372 737 5687
    Faculty address: 
    Ülikooli 18, rooms 102, 104, 209, 210, 50090 Tartu
  • Office of Academic Affairs
    Faculty phone: 
    +372 737 5620
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Procurement Office
    Faculty phone: 
    +372 737 6632
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Rector's Strategy Office
    Faculty phone: 
    +372 737 5600
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Student Council
    Faculty phone: 
    +372 737 5400
    Faculty address: 
    Ülikooli 18b, 51005 Tartu
Other Units
  • University of Tartu Academic Sports Club
    Faculty phone: 
    +372 737 5371
    Faculty address: 
    Ujula 4, 51008 Tartu
  • Tartu Student Village
    Faculty phone: 
    +372 740 9959
    Faculty address: 
    Narva mnt 25, 51013 Tartu
  • Tartu Students’ Club
    Faculty phone: 
    +372 730 2400
    Faculty address: 
    Kalevi 24, 51010 Tartu
  • University of Tartu Press
    Faculty phone: 
    +372 737 5945
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Tartu University Hospital
    Faculty address: 
    L. Puusepa 1a, 50406 Tartu
  • University of Tartu Foundation
    Faculty phone: 
    +372 737 5852
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • View all other units

Contacts of UT units

Faculty of Arts and Humanities
Faculty phone: 
+372 737 5341
Faculty address: 
Jakobi 2, rooms 116–121, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5341
    Faculty address: 
    Jakobi 2, rooms 116–121, 51005 Tartu
  • Institute of History and Archaeology
    Faculty phone: 
    +372 737 5651
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Estonian and General Linguistics
    Faculty phone: 
    +372 737 5221
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Philosophy and Semiotics
    Faculty phone: 
    +372 737 5314
    Faculty address: 
    Jakobi 2, rooms 309–352, 51005 Tartu
  • Institute of Cultural Research
    Faculty phone: 
    (+372) 737 5223
    Faculty address: 
    Ülikooli 16, 51003 Tartu
  • School of Theology and Religious Studies
    Faculty phone: 
    +372 737 5301
    Faculty address: 
    Ülikooli 18–310, 50090 Tartu
  • College of Foreign Languages and Cultures
    Faculty address: 
    Lossi 3, 51003 Tartu
  • Viljandi Culture Academy
    Faculty phone: 
    +372 435 5232
    Faculty address: 
    Posti 1, 71004 Viljandi
Faculty of Social Sciences
Faculty phone: 
+372 737 5957
Faculty address: 
Lossi 36, 51003 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5900
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Institute of Education
    Faculty phone: 
    +372 737 6440
    Faculty address: 
    Salme 1a–29, 50103 Tartu
  • Johan Skytte Institute of Political Studies
    Faculty phone: 
    +372 737 5582
    Faculty address: 
    Lossi 36–301, 51003 Tartu
  • School of Economics and Business Administration
    Faculty phone: 
    +372 737 6310
    Faculty address: 
    J. Liivi 4, 50409 Tartu
  • Institute of Psychology
    Faculty phone: 
    +372 737 5902
    Faculty address: 
    Näituse 2, 50409 Tartu
  • School of Law
    Faculty phone: 
    +372 737 5390
    Faculty address: 
    Näituse 20–324, 50409 Tartu
  • Institute of Social Studies
    Faculty phone: 
    +372 737 5188
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Narva College
    Faculty phone: 
    +372 740 1900
    Faculty address: 
    Raekoja plats 2, 20307 Narva
  • Pärnu College
    Faculty phone: 
    +372 445 0520
    Faculty address: 
    Ringi 35, 80012 Pärnu
Faculty of Medicine
Faculty phone: 
+372 737 5326
Faculty address: 
Ravila 19, 50411 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5326
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Biomedicine and Translational Medicine
    Faculty phone: 
    +372 737 4210
    Faculty address: 
    Biomeedikum, Ravila 19, 50411 Tartu
  • Institute of Pharmacy
    Faculty phone: 
    +372 737 5286
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Dentistry
    Faculty phone: 
    +372 731 9856
    Faculty address: 
    Raekoja plats 6, 51003 Tartu
  • Institute of Clinical Medicine
    Faculty phone: 
    +372 737 5323
    Faculty address: 
    L. Puusepa 8, 50406 Tartu
  • Institute of Family Medicine and Public Health
    Faculty phone: 
    +372 737 4190
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Sport Sciences and Physiotherapy
    Faculty phone: 
    +372 737 5360
    Faculty address: 
    Jakobi 5–205, 51005 Tartu
Faculty of Science and Technology
Faculty phone: 
+372 737 5820
Faculty address: 
Vanemuise 46–208, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5820
    Faculty address: 
    Vanemuise 46–208, 51005 Tartu
  • Institute of Computer Science
    Faculty phone: 
    +372 737 5445
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Estonian Marine Institute
    Faculty phone: 
    +372 671 8902
    Faculty address: 
    Mäealuse 14, 12618 Tallinn
  • Institute of Physics
    Faculty address: 
    W. Ostwaldi 1, 50411 Tartu
  • Institute of Chemistry
    Faculty phone: 
    +372 737 5261
    Faculty address: 
    Ravila 14a, 50411 Tartu
  • Institute of Mathematics and Statistics
    Faculty phone: 
    +372 737 5860
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Institute of Molecular and Cell Biology
    Faculty phone: 
    +372 737 5011
    Faculty address: 
    Riia 23, 23b–134, 51010 Tartu
  • Tartu Observatory
    Faculty phone: 
    +372 737 4510
    Faculty address: 
    Observatooriumi 1, Tõravere, 61602 Tartumaa
  • Institute of Technology
    Faculty phone: 
    +372 737 4800
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Ecology and Earth Sciences
    Faculty phone: 
    +372 737 5835
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Institutions
  • Library
    Faculty phone: 
    +372 737 5702
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Youth Academy
    Faculty phone: 
    +372 737 5581
    Faculty address: 
    Uppsala 10, 51003 Tartu
  • Institute of Genomics
    Faculty phone: 
    +372 737 4000
    Faculty address: 
    Riia 23b, 51010 Tartu
  • Museum
    Faculty phone: 
    +372 737 5674
    Faculty address: 
    Lossi 25, 51003 Tartu
  • University of Tartu Natural History Museum and Botanical Garden
    Faculty phone: 
    +372 737 6076
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Support Units
  • Administrative Office
    Faculty phone: 
    +372 737 5606
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Centre for Entrepreneurship and Innovation
    Faculty phone: 
    +372 737 6339
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • University Office in Tallinn
    Faculty phone: 
    +372 737 6600
    Faculty address: 
    Teatri väljak 3, 10143 Tallinn
  • Estates Office
    Faculty phone: 
    +372 737 5137
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Finance Office
    Faculty phone: 
    +372 737 5125
    Faculty address: 
    Jakobi 4, 51005 Tartu
  • Grant Office
    Faculty phone: 
    +372 737 6215
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • Information Technology Office
    Faculty phone: 
    +372 737 6000, IT-help: +372 737 5500
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Human Resources Office
    Faculty phone: 
    +372 737 5145
    Faculty address: 
    Ülikooli 18, rooms 302 and 304, 50090 Tartu
  • Internal Audit Office
    Faculty address: 
    Ülikooli 17–103, 51005 Tartu
  • Marketing and Communication Office
    Faculty phone: 
    +372 737 5687
    Faculty address: 
    Ülikooli 18, rooms 102, 104, 209, 210, 50090 Tartu
  • Office of Academic Affairs
    Faculty phone: 
    +372 737 5620
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Procurement Office
    Faculty phone: 
    +372 737 6632
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Rector's Strategy Office
    Faculty phone: 
    +372 737 5600
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Student Council
    Faculty phone: 
    +372 737 5400
    Faculty address: 
    Ülikooli 18b, 51005 Tartu
Other Units
  • University of Tartu Academic Sports Club
    Faculty phone: 
    +372 737 5371
    Faculty address: 
    Ujula 4, 51008 Tartu
  • Tartu Student Village
    Faculty phone: 
    +372 740 9959
    Faculty address: 
    Narva mnt 25, 51013 Tartu
  • Tartu Students’ Club
    Faculty phone: 
    +372 730 2400
    Faculty address: 
    Kalevi 24, 51010 Tartu
  • University of Tartu Press
    Faculty phone: 
    +372 737 5945
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Tartu University Hospital
    Faculty address: 
    L. Puusepa 1a, 50406 Tartu
  • University of Tartu Foundation
    Faculty phone: 
    +372 737 5852
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • View all other units

Tutorial

INSTALLATION (SCOPA and METASCOPA)

 

 

 

Copy SCOPAv*.zip file into your computer, unzip the file: 

 

unzip SCOPAv*.zip 

 

To compile SCOPA program, use command: 

 

make 

 

in the folder where files have been unpacked. The program can be run by typing: 

 

./SCOPA

 

Copy METASCOPAv*.zip file into your computer, unzip the file: 

 

unzip METASCOPAv*.zip 

 

To compile METASCOPA program, use command: 

 

make 

 

in the folder where files have been unpacked. The program can be run by typing: 

 

./METASCOPA

 

 

INPUT FILES FOR SCOPA

 

 

For running SCOPA, you need input files in SNPTESTv.2 format. SNPTEST file formats are described here. In case of case-control type of analysis, you should have single gen and sample file, where the phenotype is coded 0=control; 1=case. Please note that SCOPA cannot currently use covariates - therefore please adjust all phenotypes for the covariates and use the residuals of the phenotypes in sample file (case and controls values will be floating numbers around 0 and 1).

 

GENOTYPE file: 

 


1 rs1 11 A T 1 0 0 1 0 0 1 0 0 


1 rs2 210 A T 0 1 0 1 0 0 1 0 0

1 rs3 300 A T 1 0 0 1 0 0 1 0 0 


1 rs4 4637 A T 1 0 0 1 0 0 1 0 0 


1 rs5 5555 A T 1 0 0 1 0 0 1 0 0 

 

(Genotype file can be gzipped, if it has *.gz extension) 
 

SAMPLE file: 

 


Sample_id Subject_id Missing Phenotype1 Phenotype2 Phenotype3

0 0 0 P P P 


1 1 0 1.24 0.331 0.41 


2 2 0 1.23 -0.3 0.42 


3 3 0 1.22 -.47 0.43 



 

This file contains data for three phenotypes. As the program cannot use covariates, please adjust your phenotypes for all the covariates and use the residuals of the phenotypes.

 

RUNNING SCOPA

 

Command line options:

./SCOPA  [--debug] [--print_covariance] [--print_complex] [--betas]

            [--print_all] [--remove_missing] --pheno_name <string> ... 

            [--imp_threshold <double>] [--missing_phenotype <string>] [-e

            <string>] -o <string> -g <string> [--chr <int>] -s <string>

            [--] [--version] [-h]

 

 

Where: 

 

   --debug

         Debug mode on (default OFF)

 

   --print_covariance

Print covariance matrix data for the model with all phenotypes. This is necessary for METASCOPA and can only be used with "--print_complex" option

         (default OFF)

 

   --print_complex

Print only the model with all phenotypes. These ful models can be meta-analysed with METASCOPA (default OFF)

 

   --betas

Print each phenotype's effect size and stderr info of all selected models into separate output file (default OFF)

 

   --print_all

     Print out all models (default OFF)

 

   --remove_missing

Remove sample if any of the phenotype values is missing. This is necessary if you want to compare models based on BIC scores (default OFF)

 

   --pheno_name <string>  (accepted multiple times)

(required)  Name of phenotype to use (use this command multiple times i.e. --pheno_name BMI --pheno_name HEIGHT etc.)

 

   --imp_threshold <double>

Imputation quality threshold (default 0)

 

   --missing_phenotype <string>

         This specifies missing data value (default NA)

 

   -e <string>,  --exclusion <string>

         This specifies marker exclusion list

 

   -o <string>,  --out <string>

         (required)  This specifies output root

 

   -g <string>,  --gen <string>

         (required)  This specifies genotype file.

 

   --chr <int>

         This specifies chromosome to be printed into chromosome column

 

   -s <string>,  --sample <string>

         (required)  This specifies sample file

 

   --,  --ignore_rest

         Ignores the rest of the labeled arguments following this flag

 

   --version

         Displays version information and exits

 

   -h,  --help

         Displays usage information and exits

 

 

SCOPA OUTPUT COLUMNS

 

 

1     Chromosome - chromosome of variant if set with --chr option. Otherwise 0

2     Position - position of variant

3     MarkerName - variant name

4     EffectAllele - effect allele (necessary for meta-analysis)

5     OtherAllele - non-effect allele (necessary for meta-analysis)

6     InfoScore -  Imputation quality measurement calculated similarly to IMPUTE2

7     HWE - p-value for HWE

8     MAF - minor allele frequency

9     N - samplesize

10    AA - genotype counts from imputed data

11    AB - genotype counts from imputed data

12    BB - genotype counts from imputed data

13    PhenotypeCount - number of phenotypes in model

14    Mask - binary mask showing the phenotypes used in current model (1-usd, 0-unused)

15    LogLikelihood - model likelihood

16    nullLogLikelihood - null model likelihood

17    LikelihoodRatio - likelyhood ratio

18    P-value - model p-value

19    BIC - Bayesian information score

20    BICnull - Bayesan iformation score for null model

21    Model - phenotypes in the order they were used in model (important for selecting covariance matrix for meta-analysis)

22    sortedModel - phenotypes in model in alphabetical order

23    beta_1 - effect size for phenotype 1

24    se_1 - stderr of effect for phenotype 1

25    beta_2 - effect size for phenotype 2

26    se_2 - stderr of effect for phenotype 2

27    beta_3 - effect size for phenotype 3

28    se_3 - stderr of effect for phenotype 3

29    cov_1_1 - inverted covariance matrix values

30    cov_1_2 - inverted covariance matrix values

31    cov_1_3 - inverted covariance matrix values

32    cov_2_2 - inverted covariance matrix values

33    cov_2_3 - inverted covariance matrix values

34    cov_3_3 - inverted covariance matrix values

INPUT FILE FOR METASCOPA

 

METASCOPA is the script for meta-analysing output files from SCOPA program. As the only input file, you will need a file listing all SCOPA *.results files, which you want to meta-analyse. Plese ote that the listed files must be gzipped. The input files must only contain single model (e.g. using option --print_complex in SCOPA) and you must have the covariance matrix between phenotypes (using option --print_covariance in SCOPA). 

 

List file metascopa.in can contain rows:

 

cohort1.result.gz

cohort2.result.gz

cohort3.result.gz

 

RUNNING METASCOPA

 

Command line options:

   ./METASCOPA  [--debug] [--ogc] [--gc] [-n <int>] [--mac <double>] [--maf <double>] [--info <double>] [--hwe <double>] -o <string> -i <string> [--] [--version] [-h]

 

 

Where: 

 

   --debug

     Debug mode enabled

 

   --gc

     Use genomic control to adjust each contibuting file for population stratification (default

     OFF)

 

   --ogc

     Use genomic control to adjust meta-analysis results for population

     stratification (default OFF)

 

   -n <int>,  --samplesize <int>

     This specifies minimum samplesize filter (default 0)

 

   --mac <double>

     This specifies minimum minor allele count filter (default 0)

 

   --maf <double>

     This specifies minimal minor allele frequency filter (default 0)

 

   --info <double>

     This specifies infoscore filter (default 0)

 

   --hwe <double>

     This specifies HWE p-value filter (default 1)

 

   -o <string>,  --out <string>

     (required)  This specifies output file

 

   -i <string>,  --input <string>

     (required)  This specifies input list file

 

   --,  --ignore_rest

     Ignores the rest of the labeled arguments following this flag.

 

   --version

     Displays version information and exits.

 

   -h,  --help

     Displays usage information and exits.

 

METASCOPA OUTPUT COLUMNS

 

 

1     MarkerName - variant name

2     EA - effect allele

3     NEA - other allele

4     CohortCount - number of cohorts having data of given variant

5     N - totalsamplesize

6     beta_0 - meta-analysed effect size of phenotype 1

7     se_0 - meta-analysed stderr of effect for phenotype 1

8     beta_1 - meta-analysed effect size of phenotype 1

9     se_1 - meta-analysed stderr of effect for phenotype 1

10    beta_2 - meta-analysed effect size of phenotype 1

11    se_2 - meta-analysed stderr of effect for phenotype 1

12    ChiSq - chi for entire model

13      Pvalue - p-value for entire model (please note that the script can only calculate p-values down to 1e-20. Lower p-values are given as 0. It is possible to get exact p-values down to ~1e-200 in R using formula:

 

p<-pchisq(ChiSq,PhenotypeCount, lower.tail=F)

ANALYSIS EXAMPLE

 

 

In the first GWAS step we would recommend testing for the full model (print_complex) as it reflects all associations with each separate phenotype and their combinations (e.g. ratios). If several datasets are available, it is recommended to also print the covariance matrix (print_covariance) and use that info for meta-analysing cohorts using METASCOPA tool. An example command line for analysing anthropometric traits would be:

 

./SCOPA --remove_missing -g  cohort1_chr1.gen --chr  1 --print_complex --betas --print_covariance --out cohort1_chr1.result -s one.sample --pheno_name height   --pheno_name weight --pheno_name hip --pheno_name waist

 

By merging all chromosomes a single output file for each cohort can be created:

 

awk '{if(NR==1 || $1!="Chromosome"){print;}}' cohort1_chr*.result | gzip -c > cohort1.result

 

These results files from contributing cohorts must be written into a file, listing all file names and then all contributing files can be meta-analysed using METASCOPA with double GC correction:

 

ls cohort1.result.gz cohort2.result.gz cohort3.result.gz > cohorts.in

 

./METASCOPA --gc --ogc --mac 10 --info 0.4 --hwe 1e-4 -i cohorts.in -o meta.results

 

As the next step, top signals from the METASCOPA output can be selected, these variants could be filtered and SCOPA analysis with “print_all” (or without print command to get only the best possible model based on model BIC scores) can be made to find the optimal set of phenotypes associated with particular variant.

 

./SCOPA --remove_missing -g  cohort1_hits.gen --out cohort1_modelselection.result -s one.sample --pheno_name height   --pheno_name weight --pheno_name hip --pheno_name waist