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| | tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi | | tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi |
| | * Even with the presence of VCF file, PED/DAT files are still needed for covariates and phenotypes. | | * Even with the presence of VCF file, PED/DAT files are still needed for covariates and phenotypes. |
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| − | == Command References ==
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| − | Data File : (-dname)
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| − | Pedigree File : (-pname)
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| − | Options:
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| − | Kinship Options : --kinGeno, --empMaf [0.05], --empMiss [0.05],
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| − | --outputX, --outputKin, --kinFile [],
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| − | --kinPrefix []
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| − | Input/Output Options : --vcf [], --groupFile [], --freqFile [],
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| − | --prefix []
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| − | VC Options : --inverseNormal, --fitSharedEnv, --fitX,
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| − | --useCovariates, --traitName []
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| − | SingleVar Tests : --SingleVarLRT, --SingleVarScore,
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| − | --SingleVarWald
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| − | Burden Tests : --SKAT, --MB, --CMC_binary, --CMC_counts
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| − | Variable Threshold Tests : --VTasymptotic, --VTpermute, --permuteMin [1000],
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| − | --permuteMax [3000000]
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| − | Other Options : --function [], --mafMin [0.00], --mafMax [0.50],
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| − | --mac [0.00], --noStop, --xLabel [X],
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| − | --Xstart [2699520], --Xend [154931044], --dosage,
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| − | --founderFreq, --h2Only, --fullResult [ON]
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| − |
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| − | Crucial Input Files:
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| − | '''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:
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| − | --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:
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| − | --SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.
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| − |
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| − | Burden Tests:
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| − | --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:
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| − | --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.
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| − | --permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.
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| − | Other Options:
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| − | --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.
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| − | --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.
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| − | --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.
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| − | --founderFreq considers founder allele frequencies in analysis.
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| − | --h2Only provides a shortcut of calculating heritability only.
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| − | --fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.
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| | == Example Command Line == | | == Example Command Line == |
