|
|
| Line 6: |
Line 6: |
| | | | |
| | ==Overview of Options== | | ==Overview of Options== |
| − |
| |
| − | Data File : (-dname)
| |
| − | Pedigree File : (-pname)
| |
| | | | |
| − | Options:
| + | Options: |
| − | Kinship Options : --kinGeno, --empMaf [0.05], --empMiss [0.05],
| + | Kinship Options : --kinGeno, --kinPedigree, --kinFile [], --kinSave, |
| − | --outputX, --outputKin, --kinFile [],
| + | --kinMaf [0.05], --kinMiss [0.05] |
| − | --kinPrefix []
| + | Input/Output Options : --ped [], --dat [], --vcf [], --noeof, |
| − | Input/Output Options : --vcf [], --groupFile [], --freqFile [],
| + | --groupFile [], --longOutput [ON], --prefix [] |
| − | --prefix []
| + | VC Options : --inverseNormal, --useCovariates, --traitName [] |
| − | VC Options : --inverseNormal, --fitSharedEnv, --fitX,
| + | Single Variant Tests : --SingleVarScore |
| − | --useCovariates, --traitName []
| + | Burden Tests : --burden, --MB, --VT, --SKAT_BETA, --SKAT_UW, |
| − | SingleVar Tests : --SingleVarLRT, --SingleVarScore,
| + | --SKAT_MB |
| − | --SingleVarWald
| + | Other Options : --freqFile [], --annotation [], --maf [0.05], |
| − | Burden Tests : --SKAT, --MB, --CMC_binary, --CMC_counts
| + | --miss [0.05], --simulate, --dosage, --founderFreq |
| − | Variable Threshold Tests : --VTasymptotic, --VTpermute, --permuteMin [1000],
| + | PhoneHome : --noPhoneHome, --phoneHomeThinning [100] |
| − | --permuteMax [3000000]
| |
| − | Other Options : --function [], --mafMin [0.00], --mafMax [0.50],
| |
| − | --mac [0.00], --noStop, --xLabel [X],
| |
| − | --Xstart [2699520], --Xend [154931044], --dosage,
| |
| − | --founderFreq, --h2Only, --fullResult [ON]
| |
| | | | |
| − | ===Crucial Input Files===
| + | === Kinship Options === |
| − | '''famRvTest''' takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html|'''Merlin'''] documentation for details.
| + | --kinGeno: kinship matrix is estimated from genotype |
| − | ===Kinship Options=== | + | --kinPedigree: kinship matrix is estimated from pedigree structure |
| − | --kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.
| + | --kinFile: kinship matrix is read from a file |
| − | --empMaf and --empMiss specifies the cutoff of minor allele frequency and genotype missing rate to filter SNPs for estimating empirical kinship matrix.
| + | --kinMaf: the maf cutoff for markers used to estimate kinship |
| − | --outputX allows you to save kinship matrix from chromosome X.
| + | --kinMiss: the genotype call rate cutoff for markers included to estimate kinship |
| − | --outputKin allows you to save the kinship matrix from autosomal matrix if --outputX is also specified.
| |
| − | --kinFile allows you to read kinship matrix from a previously saved file.
| |
| − | --kinPrefix specifies the file prefix for kinship matrices saved.
| |
| | | | |
| | ===Input/Output Options=== | | ===Input/Output Options=== |
| − | --vcf specified the name of input vcf file.
| + | --ped |
| − | --groupFile should be followed by a the name of the groupfile you want to use for gene-level associations.
| |
| − | --freqFile allows users to read allele frequencies from a file instead of estimating based on data.
| |
| − | --prefix specifies the name of file prefix for all results saved.
| |
| − | | |
| − | ===SingleVar Tests===
| |
| − | --SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.
| |
| − | | |
| − | ===Burden Tests===
| |
| − | --SKAT --MB --CMC_binary --CMC_counts are SKAT, weighted-burden test (Madsen-Browning weight), collapsing burden test and unweighted burden test based on rare allele count.
| |
| − | | |
| − | ===VT Tests===
| |
| − | --VTasymptotic performs variable threshold test and calculate asymptotic p-value.
| |
| − | --VTpermute performs variable threshold test and calculate p-value based on permutation.
| |
| − | --permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.
| |
| − | | |
| − | ===Other Options===
| |
| − | --function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests.
| |
| − | --mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.
| |
| − | --mac [0.0] specify the minimum rare allele count as one of the filters to rare variants to group.
| |
| − | --noStop indicating no stopping rule to be used in VT permutation test.
| |
| − | --xLabel [X] specifies labels for chromosome X.
| |
| − | --Xstart [2699520] and --Xend [154931044] are start and end position of non-pseudo-autosomal region.
| |
| − | --founderFreq considers founder allele frequencies in analysis.
| |
| − | --h2Only provides a shortcut of calculating heritability only.
| |
| − | --fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.
| |
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
