Reference

(to finish, sorry!)

Calculating Weightings:
--cut-weights <folder> (requires data) - prepares for calculating weights across sections

--calc-weights <folder> (requires data and --section) - calculates weights for section
--join-weights <folder> (no arguments required) - joins up weights over sections
To calculate for a second time, add --weights to each of the commands
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Calculating Kinships:

--cut-kins <folder> (requires data) - prepares for calculating kinships across regions

--calc-kins <folder> (requires data, --partition, --weights / ignore-weights YES) - calculates kinships for partition
--join-kins <folder> (no arguments required)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Simulating Data:
--make-phens <outfile> (requires --file, --her) - simulates phenotypes

--make-snps <outfile> (requires --num-samples and --num-snps) - simulates SNP data

Manipulating Kinships:
--add-grm <outfile> (requires --grm) - adds kinship matrices in the specified listfile
--sub-grm <outfile> (requires --grm) - subtracts latter kinships from first kinship in listfile

Gene-based or Regional Analysis:
--cut-genes <folder> (requires --genefile, --chunks or --chunks-bp) - divides up predictors according to the genefile, or into chunks defined either by weighting or size.

In all cases, <folder> is the folder where results will be stored, while <outfile> is the prefix of results files. Replace --file with --chiamo or --sp to specify alternative File Formats.

--workdir <folder> - if used, all locations are specified relative to this folder

Datafile Inputs:
--file/--chiamo/--sp <prefix> - specifies prefix for datafiles in chosen format

--ped-headers <numbers> - number of header columns in pedfile (default 6)
--chiamo-probs <number> - number of state probabilities in chiamofile (default 2)
--chiamo-headers <number> - number of header columns in chiamofile (default 5)
--chiamo-suffix <suffix> - suffix of chiamo genotype file (default .gen)
--missingvalue <float> - value to be considered missing (used for SP format only)
--encoding <1/2/3/4> - how allele counts are coded (default additive model)

Data Filtering Options:
--extract-index <file> - read which predictors to consider from ordered list
--keep-index <file> - read which samples to consider from list (ordered if using ped format)
--minmaf <float> - exclude predictors with MAF (mean/2) < this value
--maxmaf <float> - only use predictors with MAF (mean/2) < this value
--minvar <float> - exclude predictors with variance < this value
--minobs <float> - exclude predictors with proportion observed < this value

Subset Options (when calculating weightings):
--subset-number <number> and --subset-prefix <prefix>
will read lists of individuals from files <prefix>1, <prefix>2, ..., <prefix><number>

Genomic Partitioning (when calculating kinships):
--by-chr <YES/NO> - divide genome by chromosome
--region-number <number> and --region-prefix <prefix>

user-defined regions read from files <prefix>1, <prefix>2, ..., <prefix><number>

Other Options:
--section-length <number> - desired length of sections (default 3000)
--buffer <number> - num of predictors either side of section used as buffer (default 500)
--region-length <number> - desired length of regions (default 100,000)
--halflife <basepairs> - halflife of LD decay function (default 1,000,000)
--maxlife <basepairs> - max range of LD (default 3 x halflife)
--mincor <float> - pairwise correlations below this set to zero (default 0.01)
--maxiter <number> - max iterations used in simplex method (default 40,000)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Miscellaneous Options:

--num-samples <number> - useful for providing num samples when using ped format data
--kinship-matrix <YES/NO> - if yes, then will also write kinships as matrix
--power <float> - a predictor's effect size prior variance is its variance^float (default -1)