From Genome Analysis Wiki
Jump to navigationJump to search
1,464 bytes added
, 01:48, 14 July 2014
Line 20: |
Line 20: |
| 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 | + | |
| + | --ped: merlin format ped file. |
| + | |
| + | --dat: merlin format dat file. |
| + | |
| + | --vcf: vcf file |
| + | |
| + | --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. |
| + | |
| + | --prefix: output file prefix |
| + | |
| + | ===VC options=== |
| + | |
| + | --inverseNormal: trait will be inverse normalized before analysis |
| + | |
| + | --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. |
| + | |
| + | |
| + | === Single Variant Tests=== |
| + | |
| + | --SingleVarScore: the score test |
| + | |
| + | ===Burden Tests=== |
| + | |
| + | --burden: the unweighted burden test |
| + | |
| + | --MB: the Madsen-Browning weighted burden test |
| + | |
| + | --VT: the variable threshold test |
| + | |
| + | --SKAT_BETA: the beta density weighted SKAT test (the original test) |
| + | |
| + | --SKAT_UW: the unweighted SKAT test |
| + | |
| + | --SKAT_MB: the Madsen-Browning weighted SKAT test |
| + | |
| + | |
| + | ===Other Options=== |
| + | |
| + | --freqFile []: allow users to enter frequency of markers from a file |
| + | |
| + | --annotation: allow users to group variants based on annotation |
| + | |
| + | --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 |
| + | |
| + | --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 |
| + | |
| + | --founderFreq: use founder frequencies for grouping and weighting |