Difference between revisions of "FamRvTest command"
Shuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
||
(4 intermediate revisions by the same user not shown) | |||
Line 2: | Line 2: | ||
[[FamRvTest|'''famRvTest''' Home Page]] | [[FamRvTest|'''famRvTest''' Home Page]] | ||
+ | |||
+ | [[FamRvTest_tutorial|'''famRvTest''' Tutorial]] | ||
==Overview of Options== | ==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=== | ===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 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=== | ===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 |
Latest revision as of 01:48, 14 July 2014
Useful Pages
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