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Kinship Options:
Kinship Options:
--kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.
--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.
--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.
--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.
--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.
--kinFile allows you to read kinship matrix from a previously saved file.
--kinPrefix specifies the file prefix for kinship matrices saved.
--kinPrefix specifies the file prefix for kinship matrices saved.
Input/Output Options:
Input/Output Options:
--vcf specified the name of input vcf file.
--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.
--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.
--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.
--prefix specifies the name of file prefix for all results saved.
SingleVar Tests:
SingleVar Tests:
--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.
--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.
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.
--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:
VT Tests:
--VTasymptotic performs variable threshold test and calculate asymptotic p-value.
--VTasymptotic performs variable threshold test and calculate asymptotic p-value.
--VTpermute, --permuteMin [1000],
--VTpermute performs variable threshold test and calculate p-value based on permutation.
--permuteMax [3000000]
--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 allows the permutation in VT test --xLabel [X],
--Xstart [2699520], --Xend [154931044], --dosage,
--founderFreq, --h2Only, --fullResult [ON]
== Example Command Line ==
== Example Command Line ==
