GetSynth Files

@--------------------------------------------------------------@
|     GetSynth, A toolkit for haplotype synthesis analysis     |
|            v1.0.0            |          10/Oct/2015          |
|--------------------------------------------------------------|
|  (C) by André Lacour, CC-BY-NC-ND 4.0 International license  |
|--------------------------------------------------------------|
|  For documentation, citation & bug-report instructions:      |
|  http://sourceforge.net/projects/getsynth/                   |
@--------------------------------------------------------------@

Usage: GetSynth --bfile {basename} --tag {string} [options]

Please visit the GetSynth website for a complete descriptions of the options.

--annot-file {filename}         Path and filename of annotation file. Consists of the columns: variant-ID {string}, function {list} [, gene {list}] 
--annot-functionals {list}      List of functions that are to be considered functional, default: 
--annot-non-functionals {list}  List of functions that are to be considered non-functional, default: unknown,intron
--bfile {basename}              Path and basename of input files in binary PLINK-format, !mandatory!
--covar-file {filename}         Path and filename of covariates file
--covar-number {list}           List of covariates, separated by comma and abbreviated by hyphen, e.g. 1-3,5,6
--covar-sex                     If set, sex is used as a covariate
--filter-dprime-lower {decimal} Lower |D'| cutoff, default: 0.7
--filter-dprime-upper {decimal} Upper |D'| cutoff, default: 1
--filter-functional-only        Only consider candidate variants exclusively annotated as 'functional'
--filter-ignore-chr             Ignores that tag-variant is not on same chromosome as search region (toy parameter)
--filter-max-non-func {integer} Maximum quantity of non-functional variants in considered sets, default: -1
--filter-max-tuple {integer}    Maximum cardinality of synthesizing set, default: 5
--filter-min-func {integer}     Minimum quantity of functional variants in considered sets, default: 0
--filter-minimal-only           Only consider minimal sets, ignore supersets
--filter-noprune                Do not prune variants
--filter-prune-r2 {decimal}     Set R^2 value for pruning, default: 1.0
--filter-r2-lower {decimal}     Lower R^2 cutoff, default: 0
--filter-r2-upper {decimal}     Upper R^2 cutoff, default: 0.49
--filter-tolerance {decimal}    Tolerance factor, by which the set frequency sum may exceed the tag frequency, default: 1.2
--haplo-mhf {decimal}           Minor haplotype frequency threshold, default: 0.001
--haplo-r-cut {decimal}         Limit for correlation indicator of synthesis, default: 0.95
--help                          Give help message
--model {string}                choose model {geno, haplo, reprod}, default: 
--model-delta {decimal}         Indifference margin delta, default: tagBeta
--model-p-factor {decimal}      Factor by which an additional variant has to improve the P-value in order to be reported, default: 1
--out {basename}                Sets basename for output files, default: GetSynth
--qc-geno {decimal}             Maximum per-variant missing, default: 1
--qc-hwe {decimal}              Hardy-Weinberg test on controls, default: 1e-06
--qc-hwe-all {decimal}          Hardy-Weinberg test on all individuals, default: 1e-08
--qc-mac {integer}              Lower minor allele count cutoff, default: 2
--qc-maf {decimal}              Lower minor allele frequency cutoff, default: -1
--qc-max-maf {decimal}          Upper minor allele frequency cutoff, default: 1
--qc-mind {decimal}             Maximum per-person missing, default: 1
--qc-missing-code {integer}     Missing covariate/genotype/phenotype code, default: -99
--select-from-bp {integer}      Start scan here (in basepairs)
--select-from-bp {integer}      Start scan here (in basepairs)
--select-from-kpb {integer}     Start scan here (in kilo-basepairs)
--select-from-mbp {integer}     Start scan here (in mega-basepairs)
--select-range-bp {integer}     Scan range from tag variant (in basepairs), default: 2000000
--select-range-kpb {integer}    Scan range from tag variant (in kilo-basepairs)
--select-range-mbp {integer}    Scan range from tag variant (in mega-basepairs)
--select-to-bp {integer}        End scan here (in basepairs)
--select-to-kpb {integer}       End scan here (in kilo-basepairs)
--select-to-mbp {integer}       End scan here (in mega-basepairs)
--tag {string}                  ID of the tag variant, !mandatory!