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| ==Useful Pages== | | ==Useful Pages== |
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| [[FamRvTest|'''famRvTest''' Home Page]] | | [[FamRvTest|'''famRvTest''' Home Page]] |
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| + | [[FamRvTest_tutorial|'''famRvTest''' Tutorial]] |
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| ==Overview of Options== | | ==Overview of Options== |
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− | Data File : (-dname)
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− | Pedigree File : (-pname)
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− | 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]
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− | Other Options : --function [], --mafMin [0.00], --mafMax [0.50],
| + | ===Kinship Options === |
− | --mac [0.00], --noStop, --xLabel [X],
| + | --kinGeno: kinship matrix is estimated from genotype |
− | --Xstart [2699520], --Xend [154931044], --dosage,
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− | --founderFreq, --h2Only, --fullResult [ON]
| + | --kinPedigree: kinship matrix is estimated from pedigree structure |
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| + | --kinFile: kinship matrix is read from a file |
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| + | --kinMaf: the maf cutoff for markers used to estimate kinship |
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− | ===Crucial Input Files===
| + | --kinMiss: the genotype call rate cutoff for markers included to estimate kinship |
− | '''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.
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− | ===Kinship Options===
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− | --kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.
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− | --empMaf and --empMiss specifies the cutoff of minor allele frequency and genotype missing rate to filter SNPs for estimating empirical kinship matrix.
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− | --outputX allows you to save kinship matrix from chromosome X.
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− | --outputKin allows you to save the kinship matrix from autosomal matrix if --outputX is also specified.
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− | --kinFile allows you to read kinship matrix from a previously saved file.
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− | --kinPrefix specifies the file prefix for kinship matrices saved.
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| ===Input/Output Options=== | | ===Input/Output Options=== |
− | --vcf specified the name of input vcf file.
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− | --groupFile should be followed by a the name of the groupfile you want to use for gene-level associations.
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− | --freqFile allows users to read allele frequencies from a file instead of estimating based on data.
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− | --prefix specifies the name of file prefix for all results saved.
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− | ===SingleVar Tests=== | + | --ped: merlin format ped file. |
− | --SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.
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| + | --dat: merlin format dat file. |
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| + | --vcf: vcf file |
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| + | --groupFile: gene group file for gene level tests |
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| + | --longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also. |
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| + | --prefix: output file prefix |
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| + | ===VC options=== |
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| + | --inverseNormal: trait will be inverse normalized before analysis |
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| + | --useCovariates: covariates saved in ped file will be adjusted |
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| + | --traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed. |
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| + | |
| + | === Single Variant Tests=== |
| + | |
| + | --SingleVarScore: the score test |
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| ===Burden 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.
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− | ===VT Tests===
| + | --burden: the unweighted burden test |
− | --VTasymptotic performs variable threshold test and calculate asymptotic p-value.
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− | --VTpermute performs variable threshold test and calculate p-value based on permutation.
| + | --MB: the Madsen-Browning weighted burden test |
− | --permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.
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| + | --VT: the variable threshold test |
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| + | --SKAT_BETA: the beta density weighted SKAT test (the original test) |
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| + | --SKAT_UW: the unweighted SKAT test |
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| + | --SKAT_MB: the Madsen-Browning weighted SKAT test |
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| ===Other Options=== | | ===Other Options=== |
− | --function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests.
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− | --mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.
| + | --freqFile []: allow users to enter frequency of markers from a file |
− | --mac [0.0] specify the minimum rare allele count as one of the filters to rare variants to group.
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− | --noStop indicating no stopping rule to be used in VT permutation test.
| + | --annotation: allow users to group variants based on annotation |
− | --xLabel [X] specifies labels for chromosome X.
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− | --Xstart [2699520] and --Xend [154931044] are start and end position of non-pseudo-autosomal region.
| + | --maf: maf cutoff for markers to be grouped for gene-level tests |
− | --founderFreq considers founder allele frequencies in analysis.
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− | --h2Only provides a shortcut of calculating heritability only.
| + | --miss: the genotype calling missing rate filter before grouping variants for gene-level tests |
− | --fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.
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| + | --simulate: allows an integer for number of permutations requested in single variant score test |
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| + | --dosage: the flag to tell use dosage saved in VCF file, instead of genotype |
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| + | --founderFreq: use founder frequencies for grouping and weighting |