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
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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)
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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)
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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)