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PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
=== Kinship Options ===
===Kinship Options ===
--kinGeno: kinship matrix is estimated from genotype
--kinGeno: kinship matrix is estimated from genotype
--kinPedigree: kinship matrix is estimated from pedigree structure
--kinPedigree: kinship matrix is estimated from pedigree structure
--kinFile: kinship matrix is read from a file
--kinFile: kinship matrix is read from a file
--kinMaf: the maf cutoff for markers used to estimate kinship
--kinMaf: the maf cutoff for markers used to estimate kinship
--kinMiss: the genotype call rate cutoff for markers included to estimate kinship
--kinMiss: the genotype call rate cutoff for markers included to estimate kinship
===Input/Output Options===
===Input/Output Options===
--ped: merlin format ped file.
--ped: merlin format ped file.
--dat: merlin format dat file.
--dat: merlin format dat file.
--vcf: vcf file
--vcf: vcf file
--groupFile: gene group file for gene level tests
--groupFile: gene group file for gene level tests
--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.
--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.
--prefix: output file prefix
--prefix: output file prefix
===VC options===
===VC options===
--inverseNormal: trait will be inverse normalized before analysis
--inverseNormal: trait will be inverse normalized before analysis
--useCovariates: covariates saved in ped file will be adjusted
--useCovariates: covariates saved in ped file will be adjusted
--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.
--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.
=== Single Variant Tests===
=== Single Variant Tests===
--SingleVarScore: the score test
--SingleVarScore: the score test
===Burden Tests===
===Burden Tests===
--burden: the unweighted burden test
--burden: the unweighted burden test
--MB: the Madsen-Browning weighted burden test
--MB: the Madsen-Browning weighted burden test
--VT: the variable threshold test
--VT: the variable threshold test
--SKAT_BETA: the beta density weighted SKAT test (the original test)
--SKAT_BETA: the beta density weighted SKAT test (the original test)
--SKAT_UW: the unweighted SKAT test
--SKAT_UW: the unweighted SKAT test
--SKAT_MB: the Madsen-Browning weighted SKAT test
--SKAT_MB: the Madsen-Browning weighted SKAT test
===Other Options===
===Other Options===
--freqFile []: allow users to enter frequency of markers from a file
--freqFile []: allow users to enter frequency of markers from a file
--annotation: allow users to group variants based on annotation
--annotation: allow users to group variants based on annotation
--maf: maf cutoff for markers to be grouped for gene-level tests
--maf: maf cutoff for markers to be grouped for gene-level tests
--miss: the genotype calling missing rate filter before grouping variants for gene-level tests
--miss: the genotype calling missing rate filter before grouping variants for gene-level tests
--simulate: allows an integer for number of permutations requested in single variant score test
--simulate: allows an integer for number of permutations requested in single variant score test
--dosage: the flag to tell use dosage saved in VCF file, instead of genotype
--dosage: the flag to tell use dosage saved in VCF file, instead of genotype
--founderFreq: use founder frequencies for grouping and weighting
--founderFreq: use founder frequencies for grouping and weighting
