FamRvTest command: Difference between revisions
Shuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
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===Input/Output Options=== | ===Input/Output Options=== | ||
--ped | --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 | |||
Revision as of 01:47, 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
