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Generate Command
Default Scenarios
Small sample size, basic filtering
Large sample size, association test in linkage regions
Large sample size, association test in all chromosome
Imputation only
Input file
Please enter the External program path file:
Please enter the Plink format BED file:
Please enter the Plink format BIM file:
Please enter the Plink format FAM file:
External Frequency file:
none
your own file
ftp file
Please enter the path of freq file:
Cluster file:
none
generate
your own file
ftp file
Please enter the path of cluster file:
Please enter the name of the annotation file:
Please enter the folder of output:
Linkage Analysis
Please select Linkage function:
npl
pairs
IBD Morgan
Linkage Morgan
Please enter Linkage p-value:
Please select IBD measure:
norm
permu
Please select IBD Statistics:
Spairs
Slambda
Srobdom
Saffect
Please select Linkage Morgan function:
LM Linkage
LM Bayes
Please enter penetrance value:
Please select Linkage LOD score threshold:
IBD Sharing Analysis
Please enter IBD threshold:
Please enter sharing threshold:
Imputation
Run in user-specified intervals?
Please select imputation method:
Merlin
GIGI
Please enter number of sampled realizations in the IV file:
Please select call method:
1
2
Please enter t1 for call method:
Association
Please select method to calculate p-value:
OVPDT
FBAT
Performed in linkage regions (saving running time)?
Disease Model
Please select disease model:
Segregation scores
Compound heterozygosity
Weighted-sum statistic for unrelated samples
Weighted-sum statistic for related affected individuals
Please enter threshold score file:
Please enter disease para file:
Please enter a value(Only variants with minor allele frequency (MAF) less than this value will be analyzed):
Please enter compound rule1 value:
Please enter compound rule2 value:
Please enter compound rule3 value:
Please enter compound rule4 value:
Please enter compound rule5 value:
Assign the weight of novel variants to 1, others to 0?
Please select kin:
sibs
uncle-nephew
first cousins
second cousins
Assign the weight of novel variants to 1, others to 0?
Other option
Check the running details for the external programs?
Update Genetic Positions?
Memory saving (Merlin option)?
Please enter grid size (in cM) for the Linkage and IBD Analysis:
Please enter PLINK prune threshold (variance inflation factor, VIF) for IBD sharing or Linkage:
Please specify the bit size for PedCut and Merlin:
Please enter MC value:
Please enter burn-in value:
Please enter L-sampler value:
Submit
Please copy below command to the terminal:
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