GRANVIL | University of Tartu Institute of Genomics

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

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

GRANVIL

 

INTRODUCTION

Genome-wide studies have been very successful in identifying moderate genetic effects of common alleles. However, large portion of genetic effect has remained unidentified and alternative approaches have to be used for gaining information about uncommon and rare variants as well. In genome-wide association analysis, the power of detecting true positive genotype-phenotype associations decreases in case of low minor-allele frequency. Therefore methods, which combine the information of several markers in genomic regions, should be preferred rather than using single-marker data.

GRANVIL (Gene- or Region-based ANalysis of Variants of Intermediate and Low frequency) is an implementation of a method described by Morris and Zeggini 1 to perform rare-variant analysis of binary or quantitative phenotypes. The method is based on accumulation of minor alleles of rare or uncommon markers discovered through dense genotyping or resequencing data. Association analyses are based on gene- or other pre-defined regions, determined by analyst. 

 



[1] An evaluation of statistical approaches to rare variant analysis in genetic association studies (2010). Morris, A. P.; Zeggini, E. Genetic Epidemiology 34:188-193. 
 

 

CITATION 

Magi, Kumar, Morris: Assessing the impact of missing genotype data in rare variant association analysis. BMC Proceedings 2011

 

DOWNLOAD

GRANVIL ver. 2.1.1 (changelog)
Gene list (positions dbsnp37)
Coding region marker extraction list (positions dbsnp37)
Non-synonymous marker extraction list (positions dbsnp37)

 

INSTALLATION

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

unzip GRANVILv*.zip

To compile GRANVIL program, use command:

make

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

./GRANVIL

 

INPUT FILES

For running GRANVIL, you need input files in SNPTESTv.2 format and a GENELIST file. 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.

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 Gender Phenotype Phenotype

Q 
0 0 0 D B P 


1 1 0 1 1 4.1 


2 2 0 1 1 4.2 


3 3 0 1 0 4.3 



This file contains one co-variate (Gender) and two phenotypes: first one is case-control type (for logistic regression) and second one is a continuous phenotype (for linear regresson). In current version only continuous co-variates are enabled. Discreet co-variates can be used, if they have two classes (males=1, females=0 etc.). Adjusting for centre effect or other multi-categorious co-variate: create N-1 dummy variables coded 0 or 1 for N centers and code these variables as continuous (number 3 in second row of sample file). 


GENELIST file: 


A1 1 11 111 


A5 1 2500 27300 


A13 1 14 3000 


A15 1 9 24780 



Genelist file contains four columns: 
1. GENE ID 
2. chromosome 
3. start position in bp 
4. end position in bp 
If using file, make sure that the positions in genelist file are from the same dbSNP version as in the GEN file. 


 

RUNNING GRANVIL

Command line options:


./GRANVIL [-f ] -g -s -x [-o 
] -m [--print_gene ] ... 
[--sex ] -p [--debug] [--cov_all] 
[--cond_marker ] ... [--cond_gene ] ... 
[--cov_name ] ... [-r ] [--call_thresh 
] [--imp_thresh ] [--missing_code ] 
[--chr ] [--extract_markers ] 
[--extract_samples ] [--exclude_markers ] 
[--exclude_samples ] [--] [--version] [-h] 





Where: 



-f , --flanking 
This specifies flanking region size in kb (default 0 kb) 



-g , --gen 
(required) This specifies genotype file. Can be gzipped, but must have *.gz extension then. 



-s , --sample 
(required) This specifies sample file 



-x , --genmap 
(required) This specifies gene map file 



-o , --out 
This specifies output files root 



-m , --method 
(required) This option controls how the genotype uncertainity is 
taken into account:  (a) threshold - genotypes with probability >= 0.95 will be analysed; (b) expected - genotype dosage will be constructed based on the sum of probabilities of genotypes containing one or two copies of minor allele.   

-p , --pheno 
(required) This specifies phenotype to test 



REMOVED FROM GRANVILv2.1 --lowmem 
In case of limited memory, lowmem options can be used. If both 
genelist and genotype file are both sorted in similar manner, sorted 
option can be used (faster). If the markers are in random order, 
unsorted option must be used 



--debug 
Debug mode enabled 



--cov_all 
All covariates are used in analysis



--cov_name (accepted multiple times) 
Name of covariate to use (in case of several covariates, use this 
command multiple times i.e. --cov_name SEX --cov_name AGE etc.) 



-r , --rare_thresh 
Minor allele cutoff for defining rare variants (default 0.05)



--call_thresh 
Call-rate threshold for the best guess genotypes (default 0.9) 



--imp_thresh 
Inputation score threshold for including markers (default 0.4) 



--missing_code 
This specifies the coding for missing data (default NA) 



--chr 
All markers in genotype file are forced to be from this chromosome. 
Ignoring the first column in genotype file 

--extract_samples 
This specifies file with extracted samples 



--exclude_samples 
This specifies file with excluded samples 



--extract_markers 
This specifies file with extracted markers. Marker extraction list must be in LINKAGE map format (4 columns: chromosome, markername, genetic_distance, position) and the markers are been excluded by chromosome name and position to prevent problems with different marker namings of 1000g imputed markers. 



--exclude_markers 
This specifies file with excluded markers. Marker exclusion list must be in LINKAGE map format (4 columns: chromosome, markername, genetic_distance, position) and the markers are been excluded by chromosome name and position to prevent problems with different marker namings of 1000g imputed markers. 



--print_gene (accepted multiple times) 
Name of gene model to be printed (in case of several genes, use thiscommand multiple times) Option available in GRANVILv2.1 



--sex 
This specifies gender column name in sample file for sex stratified analysis (men=0, women=1) Option available in GRANVILv2.1 



--cond_marker (accepted multiple times) 
Name of marker to use as a covariant in conditional analysis (in case of several markers, use this command multiple times) Option available in GRANVILv2.1 



--cond_gene (accepted multiple times) 
Name of gene to use as a covariant in conditional analysis (in case of several genes, use this command multiple times) Option available in GRANVILv2.1 



--, --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. 








 

QUANTITATIVE TEST: 
./GRANVIL -g data.impute.txt -s data.sample.txt --pheno PhenotypeQ --genmap ucsc_genes_b37.txt -m expected 


 

CASE-CONTROL TEST: 
./GRANVIL -g data.impute.txt -s data.sample.txt --pheno Phenotype --genmap ucsc_genes_b37.txt -m expected

 

Output file format

Results file contains following columns: 

1. gene - gene ID 


2. marker_count - number of rare markers in gene region 


3. sample_count - number of samples in analysis 


4. rare_variant_sum - count of rare alleles found in individuals 


5. total_maf - sum of MAF of all used markers in given gene region 


6. average_maf - average MAF of used markers in given gene region (total_maf / marker_count) 


7. beta - effect size 


8. se - std. error of effect 


9. z - z-statistic 


10. p - p-value