Line 1: |
Line 1: |
− | | + | ==Overview of Options== |
− | Data File : (-dname)
| + | |
| + | Data File : (-dname) |
| Pedigree File : (-pname) | | Pedigree File : (-pname) |
| | | |
Line 21: |
Line 22: |
| --founderFreq, --h2Only, --fullResult [ON] | | --founderFreq, --h2Only, --fullResult [ON] |
| | | |
− | Crucial Input Files: | + | ===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 [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html|'''Merlin'''] documentation for details. | | '''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. |
− | 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. |
Line 31: |
Line 32: |
| --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. |
Line 37: |
Line 38: |
| --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 performs variable threshold test and calculate p-value based on permutation. | | --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. | | --permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation. |
| | | |
− | Other Options: | + | ===Other Options=== |
| --function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests. | | --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. | | --mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group. |