FamRvTest command
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Data File : (-dname) Pedigree File : (-pname) Options: Kinship Options : --kinGeno, --empMaf [0.05], --empMiss [0.05], --outputX, --outputKin, --kinFile [], --kinPrefix [] Input/Output Options : --vcf [], --groupFile [], --freqFile [], --prefix [] VC Options : --inverseNormal, --fitSharedEnv, --fitX, --useCovariates, --traitName [] SingleVar Tests : --SingleVarLRT, --SingleVarScore, --SingleVarWald Burden Tests : --SKAT, --MB, --CMC_binary, --CMC_counts Variable Threshold Tests : --VTasymptotic, --VTpermute, --permuteMin [1000], --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:
famRvTest takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to Merlin documentation for details.
Kinship Options:
--kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used. --empMaf and --empMiss specifies the cutoff of minor allele frequency and genotype missing rate to filter SNPs for estimating empirical kinship matrix. --outputX allows you to save kinship matrix from chromosome X. --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:
--vcf specified the name of input vcf file. --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.