Changes

 

                    Data File :                (-dname)

                  Data File :                (-dname)

                 Pedigree File :                (-pname)

                 Pedigree File :                (-pname)

   

   

                               --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.

  --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.

  --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.