Difference between revisions of "FamRvTest command"
Shuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
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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
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
