Difference between revisions of "FamRvTest command"

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(Overview of Options)
(Overview of Options)
 
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               PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
 
               PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
  
=== Kinship Options ===
+
===Kinship Options ===
 
--kinGeno: kinship matrix is estimated from genotype
 
--kinGeno: kinship matrix is estimated from genotype
 +
 
--kinPedigree: kinship matrix is estimated from pedigree structure
 
--kinPedigree: kinship matrix is estimated from pedigree structure
 +
 
--kinFile: kinship matrix is read from a file
 
--kinFile: kinship matrix is read from a file
 +
 
--kinMaf: the maf cutoff for markers used to estimate kinship
 
--kinMaf: the maf cutoff for markers used to estimate kinship
 +
 
--kinMiss: the genotype call rate cutoff for markers included to estimate kinship
 
--kinMiss: the genotype call rate cutoff for markers included to estimate kinship
  
 
===Input/Output Options===
 
===Input/Output Options===
 +
 
--ped: merlin format ped file.
 
--ped: merlin format ped file.
 +
 
--dat: merlin format dat file.
 
--dat: merlin format dat file.
 +
 
--vcf: vcf file
 
--vcf: vcf file
 +
 
--groupFile: gene group file for gene level tests
 
--groupFile: gene group file for gene level tests
 +
 
--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.
 
--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.
 +
 
--prefix: output file prefix
 
--prefix: output file prefix
 +
 
===VC options===
 
===VC options===
 +
 
--inverseNormal: trait will be inverse normalized before analysis
 
--inverseNormal: trait will be inverse normalized before analysis
 +
 
--useCovariates: covariates saved in ped file will be adjusted
 
--useCovariates: covariates saved in ped file will be adjusted
 +
 
--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.
 
--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.
 +
  
 
===  Single Variant Tests===
 
===  Single Variant Tests===
 +
 
--SingleVarScore: the score test
 
--SingleVarScore: the score test
 +
 
===Burden Tests===
 
===Burden Tests===
 +
 
--burden: the unweighted burden test
 
--burden: the unweighted burden test
 +
 
--MB: the Madsen-Browning weighted burden test
 
--MB: the Madsen-Browning weighted burden test
 +
 
--VT: the variable threshold test
 
--VT: the variable threshold test
 +
 
--SKAT_BETA: the beta density weighted SKAT test (the original test)
 
--SKAT_BETA: the beta density weighted SKAT test (the original test)
 +
 
--SKAT_UW: the unweighted SKAT test
 
--SKAT_UW: the unweighted SKAT test
 +
 
--SKAT_MB: the Madsen-Browning weighted SKAT test
 
--SKAT_MB: the Madsen-Browning weighted SKAT test
 +
  
 
===Other Options===
 
===Other Options===
 +
 
--freqFile []: allow users to enter frequency of markers from a file
 
--freqFile []: allow users to enter frequency of markers from a file
 +
 
--annotation: allow users to group variants based on annotation
 
--annotation: allow users to group variants based on annotation
 +
 
--maf: maf cutoff for markers to be grouped for gene-level tests
 
--maf: maf cutoff for markers to be grouped for gene-level tests
 +
 
--miss: the genotype calling missing rate filter before grouping variants for gene-level tests
 
--miss: the genotype calling missing rate filter before grouping variants for gene-level tests
 +
 
--simulate: allows an integer for number of permutations requested in single variant score test
 
--simulate: allows an integer for number of permutations requested in single variant score test
 +
 
--dosage: the flag to tell use dosage saved in VCF file, instead of genotype
 
--dosage: the flag to tell use dosage saved in VCF file, instead of genotype
 +
 
--founderFreq: use founder frequencies for grouping and weighting
 
--founderFreq: use founder frequencies for grouping and weighting

Latest revision as of 01:48, 14 July 2014

Useful Pages

famRvTest Home Page

famRvTest Tutorial

Overview of Options

Options:

       Kinship Options : --kinGeno, --kinPedigree, --kinFile [], --kinSave,
                         --kinMaf [0.05], --kinMiss [0.05]
  Input/Output Options : --ped [], --dat [], --vcf [], --noeof,
                         --groupFile [], --longOutput [ON], --prefix []
            VC Options : --inverseNormal, --useCovariates, --traitName []
  Single Variant Tests : --SingleVarScore
          Burden Tests : --burden, --MB, --VT, --SKAT_BETA, --SKAT_UW,
                         --SKAT_MB
         Other Options : --freqFile [], --annotation [], --maf [0.05],
                         --miss [0.05], --simulate, --dosage, --founderFreq
             PhoneHome : --noPhoneHome, --phoneHomeThinning [100]

Kinship Options

--kinGeno: kinship matrix is estimated from genotype

--kinPedigree: kinship matrix is estimated from pedigree structure

--kinFile: kinship matrix is read from a file

--kinMaf: the maf cutoff for markers used to estimate kinship

--kinMiss: the genotype call rate cutoff for markers included to estimate kinship

Input/Output Options

--ped: merlin format ped file.

--dat: merlin format dat file.

--vcf: vcf file

--groupFile: gene group file for gene level tests

--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.

--prefix: output file prefix

VC options

--inverseNormal: trait will be inverse normalized before analysis

--useCovariates: covariates saved in ped file will be adjusted

--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.


Single Variant Tests

--SingleVarScore: the score test

Burden Tests

--burden: the unweighted burden test

--MB: the Madsen-Browning weighted burden test

--VT: the variable threshold test

--SKAT_BETA: the beta density weighted SKAT test (the original test)

--SKAT_UW: the unweighted SKAT test

--SKAT_MB: the Madsen-Browning weighted SKAT test


Other Options

--freqFile []: allow users to enter frequency of markers from a file

--annotation: allow users to group variants based on annotation

--maf: maf cutoff for markers to be grouped for gene-level tests

--miss: the genotype calling missing rate filter before grouping variants for gene-level tests

--simulate: allows an integer for number of permutations requested in single variant score test

--dosage: the flag to tell use dosage saved in VCF file, instead of genotype

--founderFreq: use founder frequencies for grouping and weighting