RABBIT's command line interface(CLI)
See section pipeline for the description of output files.
- RABBIT's command line interface(CLI)
rabbit_simfhaplo.jlrabbit_generate_magicped.jlrabbit_magicsimulate.jlrabbit_parsebreedped.jlrabbit_vcffilter.jlrabbit_resetmap.jlrabbit_magicparse.jlrabbit_magicfilter.jlrabbit_magiccall.jlrabbit_magicmap.jlrabbit_magicmask.jlrabbit_magicimpute.jlrabbit_imputeaccuracy.jlrabbit_magicmask_impute.jlrabbit_magicreconstruct.jlrabbit_thinancestry.jlrabbit_magicscan.jl
rabbit_simfhaplo.jl
julia rabbit_simfhaplo.jl -husage: rabbit_simfhaplo.jl [--nsnp NSNP] [--nparent NPARENT]
[--isfounderinbred ISFOUNDERINBRED]
[--chrlen CHRLEN] [-o OUTFILE] [-w WORKDIR]
[-h]
Simulating founder haplotypes
optional arguments:
--nsnp NSNP total number of SNPs (type: Int64, default:
1000)
--nparent NPARENT number of parents (type: Int64, default: 4)
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--chrlen CHRLEN list of chromosome lengths (in centi-Morgan),
e.g, "[100,100]" denotes 100 cM for each of
two chromosomes (default: "[100]")
-o, --outfile OUTFILE
output filename (default: "sim_fhaplo.vcf.gz")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-h, --help show this help message and exit
rabbit_generate_magicped.jl
julia rabbit_generate_magicped.jl -husage: rabbit_generate_magicped.jl [--designcodes DESIGNCODES]
[--founders FOUNDERS]
[--subpopsizes SUBPOPSIZES] [-o OUTSTEM]
[-w WORKDIR] [-h]
Generate RABBIT-format pedigree file
optional arguments:
--designcodes DESIGNCODES
design codes for each subpopulation
--founders FOUNDERS founders for each subpopulation
--subpopsizes SUBPOPSIZES
population sizes for each subpopulation
-o, --outstem OUTSTEM
outstem of output files (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-h, --help show this help message and exit
rabbit_magicsimulate.jl
julia rabbit_magicsimulate.jl -husage: rabbit_magicsimulate.jl -g FHAPLOFILE -p PEDINFO
[--popsize POPSIZE]
[--isfounderinbred ISFOUNDERINBRED]
[--foundererror FOUNDERERROR]
[--offspringerror OFFSPRINGERROR]
[--foundermiss FOUNDERMISS]
[--offspringmiss OFFSPRINGMISS]
[--seqfrac SEQFRAC] [--seqdepth SEQDEPTH]
[--seqerror SEQERROR]
[--allelebalancemean ALLELEBALANCEMEAN]
[--allelebalancedisperse ALLELEBALANCEDISPERSE]
[--ispheno ISPHENO] [--pheno_nqtl PHENO_NQTL]
[--pheno_h2 PHENO_H2]
[--nplot_subpop NPLOT_SUBPOP] [-o OUTSTEM]
[-w WORKDIR] [-h]
Simulating genotypic data in connected multiparental populations
optional arguments:
-g, --fhaplofile FHAPLOFILE
filename for founder haplotypes including
marker map
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--popsize POPSIZE poulation size, i.e. the number of offspring
(type: Int64, default: 200)
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--foundererror FOUNDERERROR
distribution of founder allelic error rate
among markers (default: "Beta(1,199)")
--offspringerror OFFSPRINGERROR
distribution of offspring allelic error rate
among markers (default: "Beta(1,199)")
--foundermiss FOUNDERMISS
distribution of founder genotype msissing
fraction among markers (default: "Beta(1,9)")
--offspringmiss OFFSPRINGMISS
distribution of offspring genotype msissing
fraction among markers (default: "Beta(1,9)")
--seqfrac SEQFRAC fraction of markers being genotyped by
sequencing, and the rest by SNP array. (type:
Float64, default: 0.0)
--seqdepth SEQDEPTH distribution of mean read depth among markers
(default: "Gamma(2,5)")
--seqerror SEQERROR distribution of sequence read error
probability (default: "Beta(1,999)")
--allelebalancemean ALLELEBALANCEMEAN
distribution of allelic balance mean among
markers (default: "Beta(10,10)")
--allelebalancedisperse ALLELEBALANCEDISPERSE
distribution of allele balance overdispersion
among markers (default: "Exponential(0.05)")
--ispheno ISPHENO if true, simulate phenotypes (type: Bool,
default: false)
--pheno_nqtl PHENO_NQTL
number of QTLs for simulating phenotypes
(type: Int64, default: 1)
--pheno_h2 PHENO_H2 heritablity for simulating phenotypes (type:
Float64, default: 0.5)
--nplot_subpop NPLOT_SUBPOP
number of plots per subpoplation (type: Int64,
default: 10)
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-h, --help show this help message and exit
rabbit_parsebreedped.jl
julia rabbit_parsebreedped.jl -husage: rabbit_parsebreedped.jl -p PEDFILE [--fixed_nself FIXED_NSELF]
[--commentstring COMMENTSTRING]
[--delim DELIM] [-o OUTFILE] [-w WORKDIR] [-h]
Parse breed pedigree file
optional arguments:
-p, --pedfile PEDFILE
breed-format pedigree file with the first
three columns: sample, pedcode, nself
--fixed_nself FIXED_NSELF
number of selfing generations for the 3rd col
= "fixed" (type: Int64, default: 10)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
--delim DELIM delimiter separates each chunk of data within
line string (type: AbstractChar, default: ',')
-o, --outfile OUTFILE
output magicped-format pedigree file (default:
"magicped.csv")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-h, --help show this help message and exit
rabbit_vcffilter.jl
julia rabbit_vcffilter.jl -husage: rabbit_vcffilter.jl -g GENOFILE [--setmarkerid SETMARKERID]
[--delsamples DELSAMPLES] [--deldupe DELDUPE]
[--delmultiallelic DELMULTIALLELIC]
[--delmonomorphic DELMONOMORPHIC]
[--seqstrech SEQSTRECH]
[--snp_maxmiss SNP_MAXMISS]
[--snp_minmaf SNP_MINMAF]
[--commentstring COMMENTSTRING] [-o OUTSTEM]
[-w WORKDIR] [-h]
Filter for biallelic markers in vcf file
optional arguments:
-g, --genofile GENOFILE
vcf genofile
--setmarkerid SETMARKERID
if true, set markerid in format of CHROM_POS
or snp{i} with {i} being the marker index if
CHROM or POS is missing. If it is nothing,
setmarkerid = true only if markerid is
missing. (default: "nothing")
--delsamples DELSAMPLES
list of samples to be deleted (default:
"nothing")
--deldupe DELDUPE if true, delete sucessive markers that have
exactly duplicated genotypes in format of GT
(type: Bool, default: false)
--delmultiallelic DELMULTIALLELIC
delete markers with >2 alleles (type: Bool,
default: true)
--delmonomorphic DELMONOMORPHIC
delete markers with only one allele (type:
Bool, default: true)
--seqstrech SEQSTRECH
delete non-initial markers in a sequence
stretch of length <= seqstretch (in bp),
assuming marker are ordered by physical
positions. If it is not positive, no filtering
for short streches. (type: Int64, default: 0)
--snp_maxmiss SNP_MAXMISS
delete markers with missing fraction >
snp_maxmiss (type: Float64, default: 0.99)
--snp_minmaf SNP_MINMAF
delete markers with minor allele frequency <
snp_minmaf (type: Float64, default: 0.01)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
-o, --outstem OUTSTEM
outstem of output files (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-h, --help show this help message and exit
rabbit_resetmap.jl
julia rabbit_resetmap.jl -husage: rabbit_resetmap.jl -g GENOFILE --mapfile MAPFILE
[--commentstring COMMENTSTRING] [-o OUTSTEM]
[-w WORKDIR] [-h]
Replace marker map in input genofile with that of mapfile
optional arguments:
-g, --genofile GENOFILE
vcf genofile
--mapfile MAPFILE file for marker map, it can either be in VCF
format or in CSV format. For CSV-format, it
must contain at least four columns: marker,
chromosome poscm, physposbp. The values for
the last three coloumns can be missingstring
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
-o, --outstem OUTSTEM
outstem of output files (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-h, --help show this help message and exit
rabbit_magicparse.jl
julia rabbit_magicparse.jl -husage: rabbit_magicparse.jl -g GENOFILE -p PEDINFO
[--isfounderinbred ISFOUNDERINBRED]
[--formatpriority FORMATPRIORITY]
[--isphysmap ISPHYSMAP]
[--recomrate RECOMRATE]
[--isbreedped ISBREEDPED]
[--fixed_nself FIXED_NSELF]
[--commentstring COMMENTSTRING]
[--outext OUTEXT] [-o OUTSTEM] [-w WORKDIR]
[-v VERBOSE] [-h]
Parse genofile and pedfile
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--formatpriority FORMATPRIORITY
priorities of genotype formats in a decreasing
order (default: "[AD,GT]")
--isphysmap ISPHYSMAP
if true, transform physical map into genetic
map using recomrate, and overwrite the exist
genetic map. If false, keep input physical
and/or genetic map. (type: Bool, default:
false)
--recomrate RECOMRATE
constant recombation rate in cM/Mbp (type:
Float64, default: 1.0)
--isbreedped ISBREEDPED
if true, input pedinfo is a breedped-format
file instead of magicped-format pedfile for
RABBIT. If it is nothing, it is internally
set. (default: "nothing")
--fixed_nself FIXED_NSELF
number of selfing generations for the 3rd col
= "fixed" (type: Int64, default: 10)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
--outext OUTEXT extension of output genofile (default:
".vcf.gz")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_magicfilter.jl
julia rabbit_magicfilter.jl -husage: rabbit_magicfilter.jl -g GENOFILE -p PEDINFO
[--formatpriority FORMATPRIORITY]
[--isphysmap ISPHYSMAP]
[--recomrate RECOMRATE] [--model MODEL]
[--likeparameters LIKEPARAMETERS]
[--isfounderinbred ISFOUNDERINBRED]
[--chrsubset CHRSUBSET] [--snpthin SNPTHIN]
[--delmultiallelic DELMULTIALLELIC]
[--del_inconsistent DEL_INCONSISTENT]
[--min_subpop MIN_SUBPOP]
[--min_nprogeny MIN_NPROGENY]
[--snp_monosubpop SNP_MONOSUBPOP]
[--snp_mono2miss SNP_MONO2MISS]
[--snp_minmaf SNP_MINMAF]
[--snp_maxomiss SNP_MAXOMISS]
[--or_snp_maxfmiss OR_SNP_MAXFMISS]
[--offspring_maxmiss OFFSPRING_MAXMISS]
[--isfilterdupe ISFILTERDUPE]
[--offspring_maxcorr OFFSPRING_MAXCORR]
[--offspring_cutcorr OFFSPRING_CUTCORR]
[--commentstring COMMENTSTRING]
[--outext OUTEXT] [-o OUTSTEM] [-w WORKDIR]
[-v VERBOSE] [-h]
Filter markers and individuals in connected multiparental populations
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--formatpriority FORMATPRIORITY
priorities of genotype formats in a decreasing
order (default: "[AD,GT]")
--isphysmap ISPHYSMAP
if true, transform physical map into genetic
map using recomrate, and overwrite the exist
genetic map. If false, keep input physical
and/or genetic map. (type: Bool, default:
false)
--recomrate RECOMRATE
constant recombation rate in cM/Mbp (type:
Float64, default: 1.0)
--model MODEL "depmodel", "indepmodel", or "jointmodel"
specifies prior dependence of ancestral prior
process along two homologous chromosomes
within an offspring (default: "jointmodel")
--likeparameters LIKEPARAMETERS
Set error rate values in the genotypic data
model. (default: "LikeParameters()")
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--chrsubset CHRSUBSET
subset of chromosomes, with nothing denoting
all chromosomes, e.g, "[2,10]" denotes
the second and tenth chromosomes (default:
"nothing")
--snpthin SNPTHIN subset of markers by taking every snpthin-th
markers (type: Int64, default: 1)
--delmultiallelic DELMULTIALLELIC
delete markers with >2 alleles (type: Bool,
default: true)
--del_inconsistent DEL_INCONSISTENT
if true, delete markers with inconsistent
changes of founder genotypes. (type: Bool,
default: false)
--min_subpop MIN_SUBPOP
delete subpopulaions with size < min_subpop
(type: Int64, default: 1)
--min_nprogeny MIN_NPROGENY
delete founder and their progeny if the number
of progeny < min_nprogeny (type: Int64,
default: 1)
--snp_monosubpop SNP_MONOSUBPOP
monomorphic test for a subpopulation at a
marker only if #observed genotypes >=
snp_monosubpop. (type: Int64, default: 20)
--snp_mono2miss SNP_MONO2MISS
if true, offspring genotypes in each
monomorphic subpopulation are set to missing,
and otherwise only inconsistent offspring
genotypes are corrected. And if it is nothing,
offspring genotypes are not changed. (default:
"true")
--snp_minmaf SNP_MINMAF
test monomorphic for a subpopulation only if
its minor allele frequency (maf) < snp_minmaf.
And filter for markers with maf >= snp_minmaf.
(type: Float64, default: 0.05)
--snp_maxomiss SNP_MAXOMISS
filter for markers with missing fraction in
offspring <= snp_maxomiss || missing fraction
in founder < or_snp_maxfmiss (type: Float64,
default: 1.0)
--or_snp_maxfmiss OR_SNP_MAXFMISS
filter for markers with missing fraction in
offspring <= snp_maxomiss || missing fraction
in founder < or_snp_maxfmiss (type: Float64,
default: 0.0)
--offspring_maxmiss OFFSPRING_MAXMISS
delete offspring if its missing fraction >
offspring_maxmiss (type: Float64, default:
1.0)
--isfilterdupe ISFILTERDUPE
if true, keep only one of duplicated
individuals (type: Bool, default: false)
--offspring_maxcorr OFFSPRING_MAXCORR
two offspring are duplciated if their
correlation > offspring_maxcorr (type:
Float64, default: 0.99)
--offspring_cutcorr OFFSPRING_CUTCORR
pairwise offspring correlations are set zeros
if they < offspring_cutcorr (type: Float64,
default: 0.4)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
--outext OUTEXT extension of output genofile (default:
".vcf.gz")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_magiccall.jl
julia rabbit_magiccall.jl -husage: rabbit_magiccall.jl -g GENOFILE -p PEDINFO [--model MODEL]
[--likeparameters LIKEPARAMETERS]
[--threshlikeparameters THRESHLIKEPARAMETERS]
[--priorlikeparameters PRIORLIKEPARAMETERS]
[--isfounderinbred ISFOUNDERINBRED]
[--threshcall THRESHCALL]
[--israwcall ISRAWCALL]
[--isinfererror ISINFERERROR]
[--nworker NWORKER] [--outext OUTEXT]
[-o OUTSTEM] [-w WORKDIR] [-v VERBOSE] [-h]
Single marker genotype call in connected multiparental populations
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--model MODEL "depmodel", "indepmodel", or "jointmodel"
specifies prior dependence of ancestral prior
process along two homologous chromosomes
within an offspring (default: "jointmodel")
--likeparameters LIKEPARAMETERS
parameters for genotypic data model. If
isinfererror = true, parameters with values
being nothing will be inferred. (default:
"LikeParameters(peroffspringerror=0.0)")
--threshlikeparameters THRESHLIKEPARAMETERS
markers with inferred likeparameters values >
threshlikeparameters values will be deleted
(default: "ThreshLikeParameters()")
--priorlikeparameters PRIORLIKEPARAMETERS
priors for likelihood parameters (default:
"PriorLikeParameters(offspringerror=Beta(1.05,9),seqerror=Beta(1.05,9))")
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--threshcall THRESHCALL
genotye call if maximum posterior probability
> threshcall (default: "nothing")
--israwcall ISRAWCALL
if true, perform raw genotype calling (type:
Bool, default: false)
--isinfererror ISINFERERROR
if true, infer marker specific error rates. If
it is nothing, isinfererror = !israwcall
(default: "nothing")
--nworker NWORKER number of parallel workers for computing among
chromosomes (type: Int64, default: 1)
--outext OUTEXT extension of output genofile (default:
".vcf.gz")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_magicmap.jl
julia rabbit_magicmap.jl -husage: rabbit_magicmap.jl -g GENOFILE -p PEDINFO [--ncluster NCLUSTER]
[--minncluster MINNCLUSTER]
[--maxncluster MAXNCLUSTER]
[--minsilhouette MINSILHOUETTE]
[--formatpriority FORMATPRIORITY]
[--model MODEL]
[--likeparameters LIKEPARAMETERS]
[--isfounderinbred ISFOUNDERINBRED]
[--snpthin SNPTHIN]
[--ispermmarker ISPERMMARKER]
[--isdupebinning ISDUPEBINNING]
[--mincomponentsize MINCOMPONENTSIZE]
[--minlodcluster MINLODCLUSTER]
[--minlodorder MINLODORDER]
[--knncluster KNNCLUSTER]
[--knnorder KNNORDER] [--nworker NWORKER]
[--commentstring COMMENTSTRING] [-o OUTSTEM]
[-w WORKDIR] [-v VERBOSE] [-h]
Genetic map construction in connected multiparental populations
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--ncluster NCLUSTER number of linkage groups. If it is nothing,
ncluster will be inferred in the range of
[minncluster, maxncluster] (default:
"nothing")
--minncluster MINNCLUSTER
min number of linkage groups. If it is
nothing, minncluster is set to 1 if ncluster =
nothing and otherwise it is set to ncluster
(default: "nothing")
--maxncluster MAXNCLUSTER
max number of linkage groups. If it is
nothing, maxncluster is set to 30 if ncluster
= nothing and otherwise it is set to ncluster
(default: "nothing")
--minsilhouette MINSILHOUETTE
delete markers withg silhouette scores <
minsilhouette (type: Float64, default: 0.0)
--formatpriority FORMATPRIORITY
priorities of genotype formats in a decreasing
order (default: "[GT,AD]")
--model MODEL "depmodel", "indepmodel", or "jointmodel"
specifies prior dependence of ancestral prior
process along two homologous chromosomes
within an offspring (default: "jointmodel")
--likeparameters LIKEPARAMETERS
Set error rate values in the genotypic data
model. (default: "LikeParameters()")
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--snpthin SNPTHIN thin markers by taking every snpthin-th
markers (type: Int64, default: 1)
--ispermmarker ISPERMMARKER
if true, permute input marker ordering (type:
Bool, default: true)
--isdupebinning ISDUPEBINNING
if ture, bin duplicate marker (default:
"false")
--mincomponentsize MINCOMPONENTSIZE
connectecd components of size <
mincomponentsize are removed. If it is
nothing, it is internally set. (default:
"nothing")
--minlodcluster MINLODCLUSTER
minimum lod score for clustering. If it is
nothing, it is internally set. (default:
"nothing")
--minlodorder MINLODORDER
minimum lod score for ordering. If it is
nothing, it is internally set. (default:
"nothing")
--knncluster KNNCLUSTER
number of nearest neighbors for clustering. If
-1, it is set to the nearest integer of
0.1*#markers (type: Int64, default: -1)
--knnorder KNNORDER number of nearest neighbors for ordering. If
-1, it is set to the nearest integer of
sqrt(#markers) (type: Int64, default: -1)
--nworker NWORKER number of parallel workers for computing
(type: Int64, default: 1)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_magicmask.jl
julia rabbit_magicmask.jl -husage: rabbit_magicmask.jl -g GENOFILE -p PEDINFO
[--isfounderinbred ISFOUNDERINBRED]
[--formatpriority FORMATPRIORITY]
[--isphysmap ISPHYSMAP]
[--recomrate RECOMRATE]
[--foundermask FOUNDERMASK]
[--offspringmask OFFSPRINGMASK]
[--skipmarker SKIPMARKER] [--minread MINREAD]
[--commentstring COMMENTSTRING]
[--outext OUTEXT] [-o OUTSTEM] [-w WORKDIR]
[-v VERBOSE] [-h]
Mask genotypes for evaluating imputation
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--formatpriority FORMATPRIORITY
priorities of genotype formats in a decreasing
order (default: "[AD,GT]")
--isphysmap ISPHYSMAP
if true, transform physical map into genetic
map using recomrate, and overwrite the exist
genetic map. If false, keep input physical
and/or genetic map. (type: Bool, default:
false)
--recomrate RECOMRATE
constant recombation rate in cM/Mbp (type:
Float64, default: 1.0)
--foundermask FOUNDERMASK
fraction of observed founder genotypes to be
masked (type: Float64, default: 0.1)
--offspringmask OFFSPRINGMASK
fraction of observed offspring genotypes to be
masked (type: Float64, default: 0.1)
--skipmarker SKIPMARKER
skip masking markers with offspring missing
fraction >= skipmarker (type: Float64,
default: 0.99)
--minread MINREAD skip masking genotypes with #reads < minread
(type: Int64, default: 10)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
--outext OUTEXT extension of output genofile (default:
".vcf.gz")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_magicimpute.jl
julia rabbit_magicimpute.jl -husage: rabbit_magicimpute.jl -g GENOFILE -p PEDINFO
[--formatpriority FORMATPRIORITY]
[--isphysmap ISPHYSMAP]
[--recomrate RECOMRATE] [--model MODEL]
[--likeparameters LIKEPARAMETERS]
[--threshlikeparameters THRESHLIKEPARAMETERS]
[--priorlikeparameters PRIORLIKEPARAMETERS]
[--isfounderinbred ISFOUNDERINBRED]
[--chrsubset CHRSUBSET] [--snpthin SNPTHIN]
[--target TARGET]
[--threshimpute THRESHIMPUTE]
[--byfounder BYFOUNDER]
[--isrepeatimpute ISREPEATIMPUTE]
[--nrepeatmin NREPEATMIN]
[--nrepeatmax NREPEATMAX] [--mapfile MAPFILE]
[--iscorrectfounder ISCORRECTFOUNDER]
[--phasealg PHASEALG]
[--isdelmarker ISDELMARKER]
[--isinfererror ISINFERERROR]
[--tukeyfence TUKEYFENCE]
[--isordermarker ISORDERMARKER]
[--inittemperature INITTEMPERATURE]
[--coolrate COOLRATE]
[--isspacemarker ISSPACEMARKER]
[--trimcm TRIMCM]
[--skeletonsize SKELETONSIZE]
[--nworker NWORKER]
[--commentstring COMMENTSTRING]
[--outext OUTEXT] [-o OUTSTEM] [-w WORKDIR]
[-t TEMPDIRECTORY] [-v VERBOSE] [-h]
Genotype imputation in connected multiparental populations
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--formatpriority FORMATPRIORITY
priorities of genotype formats in a decreasing
order (default: "[AD,GT]")
--isphysmap ISPHYSMAP
if true, transform physical map into genetic
map using recomrate, and overwrite the exist
genetic map. If false, keep input physical
and/or genetic map. (type: Bool, default:
false)
--recomrate RECOMRATE
constant recombation rate in cM/Mbp (type:
Float64, default: 1.0)
--model MODEL "depmodel", "indepmodel", or "jointmodel"
specifies prior dependence of ancestral prior
process along two homologous chromosomes
within an offspring (default: "jointmodel")
--likeparameters LIKEPARAMETERS
parameters for genotypic data model. If
isinfererror = true, parameters with values
being nothing will be inferred. (default:
"LikeParameters()")
--threshlikeparameters THRESHLIKEPARAMETERS
markers with inferred likeparameters values >
threshlikeparameters values will be deleted
(default: "ThreshLikeParameters()")
--priorlikeparameters PRIORLIKEPARAMETERS
priors for likelihood parameters (default:
"PriorLikeParameters()")
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--chrsubset CHRSUBSET
subset of chromosomes, with nothing denoting
all chromosomes, e.g, "[2,10]" denotes
the second and tenth chromosomes (default:
"nothing")
--snpthin SNPTHIN subset of markers by taking every snpthin-th
markers (type: Int64, default: 1)
--target TARGET imputing target: "all", "founder", or
"offspring" (default: "all")
--threshimpute THRESHIMPUTE
impute offspring if maximum posterior
probability > threshimpute (type: Float64,
default: 0.9)
--byfounder BYFOUNDER
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (type: Int64,
default: 0)
--isrepeatimpute ISREPEATIMPUTE
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (default: "false")
--nrepeatmin NREPEATMIN
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (type: Int64,
default: 3)
--nrepeatmax NREPEATMAX
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (type: Int64,
default: 6)
--mapfile MAPFILE if it is nothing, use the marker map in the
input genofile, and otherwise reset genetic
marker map by that in mapfile. The mapfile can
either be in VCF format or in CSV format. For
VCF format, genetic map is provided in the
"INFO" column using keywords "LINKAGEGROUP"
and "POSCM". For CSV-format, it must contain
at least five columns: "marker",
"linkagegroup", "poscm", "physchrom", and
"physposbp", where missing values are
represented by "NA". If there exist columns
"binno" and "represent", markers with the same
"binno" are binned with the represent being
the marker with non-zero "represent". All the
rest columns are ignored. (default:
"nothing")
--iscorrectfounder ISCORRECTFOUNDER
if true, perform parental error correction. If
it is nothing, iscorrectfounder=true if
model=depmodel or offspring do not have
genotypes in AD format (default: "nothing")
--phasealg PHASEALG If phasealg=forwardbackward, the output
diplotype probabilities (in format GP),
corresonding to the phased genotypes 0|0, 0|1,
1|0, and 1|1, are caculated based on the
forward-backward algorithm, and the output
phased offspring genotypes (in format GT) are
given by those with the largest diplotype
probabilities if they are greater than
threshcall. If phasealg=viterbi, the output
diplotype probabilities (GP) are set to those
of phasealg=forwardbackward, and the output
phased genotypes (GT) are caculated based on
the Viterbi algorithm. If phasealg=unphase,
the output genotype probabilities (GP),
corresonding to the unphased genotypes 0/0,
0/1, and 1/1, are calculated by transforming
the posterior diplotype probabilities of
phasealg=forwardbackward, and the output
unphased genotypes (GT) are given by those
with the largest genotype probabilities if
they are greater than threshcall. (default:
"unphase")
--isdelmarker ISDELMARKER
if true, perform marker deletion (type: Bool,
default: true)
--isinfererror ISINFERERROR
if true, infer marker specific error rates.
If it is nothing, isinfererror=true if model ≠
depmodel or isspacemarker = true. It is
necessary to set isinfererror = true for
accurately imputing sequence data in
heterozygous populations. (default: "true")
--tukeyfence TUKEYFENCE
tukeyfence for detecting outlier error rates
(type: Float64, default: 3.0)
--isordermarker ISORDERMARKER
if true, refine local marker ordering, If it
is nothing, isordermarker=true only if mapfile
exists. (default: "nothing")
--inittemperature INITTEMPERATURE
initial temperature of annealing algorithm for
marker ordering. If it is nothing,
inittemperature=2.0 if isordermarker and
otherwise 0.0 (default: "nothing")
--coolrate COOLRATE temperature is mutiplied by coolrate after
each iteration of annealing agrogrithm (type:
Float64, default: 0.7)
--isspacemarker ISSPACEMARKER
if true, refine inter-marker distances. If it
is nothing, isspacemarker=true if mapfile
exists or isordermarker=true or
isphysmap=true. (default: "nothing")
--trimcm TRIMCM remove markers of each segment with distances
to the flanking markers > trimcm (cM) (type:
Float64, default: 20.0)
--skeletonsize SKELETONSIZE
number of skeleton markers for piecewisely
re-scaling inter-marker distances. If it is
nothing, skeletonsize is set to the number of
marers with distinct positions. (default:
"nothing")
--nworker NWORKER number of parallel workers for computing among
chromosomes (type: Int64, default: 1)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
--outext OUTEXT extension of output genofile (default:
".vcf.gz")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-t, --tempdirectory TEMPDIRECTORY
tempdirectory directory for intermediate
results (default: tempdir())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_imputeaccuracy.jl
julia rabbit_imputeaccuracy.jl -husage: rabbit_imputeaccuracy.jl -f TRUEGENOFILE -g IMPUTEDGENOFILE
-p PEDINFO [-o OUTSTEM] [-w WORKDIR]
[-v VERBOSE] [-h]
Calculate imputation accuracy per parent and per subpopulation
optional arguments:
-f, --truegenofile TRUEGENOFILE
true genofile resulting from `magicsimulate`
or magicmask_reversed genofile resulting from
`magicmask`
-g, --imputedgenofile IMPUTEDGENOFILE
imputed genofile resulting from `magicimpute`
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_magicmask_impute.jl
julia rabbit_magicmask_impute.jl -husage: rabbit_magicmask_impute.jl -g GENOFILE -p PEDINFO
[--formatpriority FORMATPRIORITY]
[--isphysmap ISPHYSMAP]
[--recomrate RECOMRATE]
[--foundermask FOUNDERMASK]
[--offspringmask OFFSPRINGMASK]
[--skipmarker SKIPMARKER] [--minread MINREAD]
[--model MODEL]
[--likeparameters LIKEPARAMETERS]
[--threshlikeparameters THRESHLIKEPARAMETERS]
[--priorlikeparameters PRIORLIKEPARAMETERS]
[--isfounderinbred ISFOUNDERINBRED]
[--chrsubset CHRSUBSET] [--snpthin SNPTHIN]
[--target TARGET]
[--threshimpute THRESHIMPUTE]
[--byfounder BYFOUNDER]
[--isrepeatimpute ISREPEATIMPUTE]
[--nrepeatmin NREPEATMIN]
[--nrepeatmax NREPEATMAX] [--mapfile MAPFILE]
[--iscorrectfounder ISCORRECTFOUNDER]
[--phasealg PHASEALG]
[--isdelmarker ISDELMARKER]
[--isinfererror ISINFERERROR]
[--tukeyfence TUKEYFENCE]
[--isordermarker ISORDERMARKER]
[--inittemperature INITTEMPERATURE]
[--coolrate COOLRATE]
[--isspacemarker ISSPACEMARKER]
[--trimcm TRIMCM]
[--skeletonsize SKELETONSIZE]
[--nworker NWORKER]
[--commentstring COMMENTSTRING]
[--outext OUTEXT] [-o OUTSTEM] [-w WORKDIR]
[-t TEMPDIRECTORY] [-v VERBOSE] [-h]
Genotype masking and imputation in connected multiparental populations
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--formatpriority FORMATPRIORITY
priorities of genotype formats in a decreasing
order (default: "[AD,GT]")
--isphysmap ISPHYSMAP
if true, transform physical map into genetic
map using recomrate, and overwrite the exist
genetic map. If false, keep input physical
and/or genetic map. (type: Bool, default:
false)
--recomrate RECOMRATE
constant recombation rate in cM/Mbp (type:
Float64, default: 1.0)
--foundermask FOUNDERMASK
fraction of observed founder genotypes to be
masked (type: Float64, default: 0.1)
--offspringmask OFFSPRINGMASK
fraction of observed offspring genotypes to be
masked (type: Float64, default: 0.1)
--skipmarker SKIPMARKER
skip masking markers with offspring missing
fraction >= skipmarker (type: Float64,
default: 0.99)
--minread MINREAD skip masking genotypes with #reads < minread
(type: Int64, default: 10)
--model MODEL "depmodel", "indepmodel", or "jointmodel"
specifies prior dependence of ancestral prior
process along two homologous chromosomes
within an offspring (default: "jointmodel")
--likeparameters LIKEPARAMETERS
parameters for genotypic data model. If
isinfererror = true, parameters with values
being nothing will be inferred. (default:
"LikeParameters()")
--threshlikeparameters THRESHLIKEPARAMETERS
markers with inferred likeparameters values >
threshlikeparameters values will be deleted
(default: "ThreshLikeParameters()")
--priorlikeparameters PRIORLIKEPARAMETERS
priors for likelihood parameters (default:
"PriorLikeParameters()")
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--chrsubset CHRSUBSET
subset of chromosomes, with nothing denoting
all chromosomes, e.g, "[2,10]" denotes
the second and tenth chromosomes (default:
"nothing")
--snpthin SNPTHIN subset of markers by taking every snpthin-th
markers (type: Int64, default: 1)
--target TARGET imputing target: "all", "founder", or
"offspring" (default: "all")
--threshimpute THRESHIMPUTE
impute offspring if maximum posterior
probability > threshimpute (type: Float64,
default: 0.9)
--byfounder BYFOUNDER
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (type: Int64,
default: 0)
--isrepeatimpute ISREPEATIMPUTE
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (default: "nothing")
--nrepeatmin NREPEATMIN
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (type: Int64,
default: 3)
--nrepeatmax NREPEATMAX
alternatively impute founder blocks (a
parition of founders). If byfounder==-1,
impute all founders simulteneously. If
byfounder==0, partition is based on the
founders of each subpopulation. If
byfounder>0, the size of each block <=
byfounder and each block is the subset of a
subpopulation's founders. (type: Int64,
default: 6)
--mapfile MAPFILE if it is nothing, use the marker map in the
input genofile, and otherwise reset genetic
marker map by that in mapfile. The mapfile can
either be in VCF format or in CSV format. For
VCF format, genetic map is provided in the
"INFO" column using keywords "LINKAGEGROUP"
and "POSCM". For CSV-format, it must contain
at least five columns: "marker",
"linkagegroup", "poscm", "physchrom", and
"physposbp", where missing values are
represented by "NA". If there exist columns
"binno" and "represent", markers with the same
"binno" are binned with the represent being
the marker with non-zero "represent". All the
rest columns are ignored. (default:
"nothing")
--iscorrectfounder ISCORRECTFOUNDER
if true, perform parental error correction. If
it is nothing, iscorrectfounder=true if
model=depmodel or isinfererror=true or
offspring do not have genotypes in AD format
(default: "nothing")
--phasealg PHASEALG If phasealg=forwardbackward, the output
diplotype probabilities (in format GP),
corresonding to the phased genotypes 0|0, 0|1,
1|0, and 1|1, are caculated based on the
forward-backward algorithm, and the output
phased offspring genotypes (in format GT) are
given by those with the largest diplotype
probabilities if they are greater than
threshcall. If phasealg=viterbi, the output
diplotype probabilities (GP) are set to those
of phasealg=forwardbackward, and the output
phased genotypes (GT) are caculated based on
the Viterbi algorithm. If phasealg=unphase,
the output genotype probabilities (GP),
corresonding to the unphased genotypes 0/0,
0/1, and 1/1, are calculated by transforming
the posterior diplotype probabilities of
phasealg=forwardbackward, and the output
unphased genotypes (GT) are given by those
with the largest genotype probabilities if
they are greater than threshcall. (default:
"unphase")
--isdelmarker ISDELMARKER
if true, perform marker deletion (type: Bool,
default: true)
--isinfererror ISINFERERROR
if true, infer marker specific error rates.
If it is nothing, isinfererror=true if model ≠
depmodel or isspacemarker = true. It is
necessary to set isinfererror = true for
accurately imputing sequence data in
heterozygous populations. (default: "true")
--tukeyfence TUKEYFENCE
tukeyfence for detecting outlier error rates
(type: Float64, default: 3.0)
--isordermarker ISORDERMARKER
if true, refine local marker ordering. If it
is nothing, isordermarker=true only if mapfile
exists. (default: "nothing")
--inittemperature INITTEMPERATURE
initial temperature of annealing algorithm for
marker ordering. If it is nothing,
inittemperature=2.0 if isordermarker and
otherwise 0.0 (default: "nothing")
--coolrate COOLRATE temperature is mutiplied by coolrate after
each iteration of annealing agrogrithm (type:
Float64, default: 0.7)
--isspacemarker ISSPACEMARKER
if true, refine inter-marker distances. If it
is nothing, isspacemarker=true if mapfile
exists or isordermarker=true or
isphysmap=true. (default: "nothing")
--trimcm TRIMCM remove markers of each segment with distances
to the flanking markers > trimcm (cM) (type:
Float64, default: 20.0)
--skeletonsize SKELETONSIZE
number of skeleton markers for piecewisely
re-scaling inter-marker distances. If it is
nothing, skeletonsize is set to the number of
marers with distinct positions. (default:
"nothing")
--nworker NWORKER number of parallel workers for computing among
chromosomes (type: Int64, default: 1)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
--outext OUTEXT extension of output genofile (default:
".vcf.gz")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-t, --tempdirectory TEMPDIRECTORY
tempdirectory directory for intermediate
results (default: tempdir())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_magicreconstruct.jl
julia rabbit_magicreconstruct.jl -husage: rabbit_magicreconstruct.jl -g GENOFILE -p PEDINFO
[--formatpriority FORMATPRIORITY]
[--isphysmap ISPHYSMAP]
[--recomrate RECOMRATE] [--model MODEL]
[--likeparameters LIKEPARAMETERS]
[--isfounderinbred ISFOUNDERINBRED]
[--chrsubset CHRSUBSET] [--snpthin SNPTHIN]
[--hmmalg HMMALG]
[--isignorephase ISIGNOREPHASE]
[--nworker NWORKER]
[--commentstring COMMENTSTRING] [-o OUTSTEM]
[-w WORKDIR] [-t TEMPDIRECTORY]
[--nplot_subpop NPLOT_SUBPOP] [-v VERBOSE]
[-h]
Haplotype reconstruction in connected multiparental populations
optional arguments:
-g, --genofile GENOFILE
filename for genotypic data file
-p, --pedinfo PEDINFO
pedigree information: filename or stringcode
--formatpriority FORMATPRIORITY
priorities of genotype formats in a decreasing
order (default: "[GP,AD,GT]")
--isphysmap ISPHYSMAP
if true, transform physical map into genetic
map using recomrate, and overwrite the exist
genetic map. If false, keep input physical
and/or genetic map. (type: Bool, default:
false)
--recomrate RECOMRATE
constant recombation rate in cM/Mbp (type:
Float64, default: 1.0)
--model MODEL "depmodel", "indepmodel", or "jointmodel"
specifies prior dependence of ancestral prior
process along two homologous chromosomes
within an offspring (default: "jointmodel")
--likeparameters LIKEPARAMETERS
Set error rate values in the genotypic data
model. (default: "LikeParameters()")
--isfounderinbred ISFOUNDERINBRED
if true, founders are inbred, and otherwise
outbred (type: Bool, default: true)
--chrsubset CHRSUBSET
subset of chromosomes, with nothing denoting
all chromosomes, e.g, "[2,10]" denotes
the second and tenth chromosomes (default:
"nothing")
--snpthin SNPTHIN subset of markers by taking every snpthin-th
markers (type: Int64, default: 1)
--hmmalg HMMALG HMM alogrithm must be either forwardbackward
or viterbi (default: "forwardbackward")
--isignorephase ISIGNOREPHASE
if true, the phases of offspring genotypes are
ignored. (type: Bool, default: false)
--nworker NWORKER number of parallel workers for computing among
chromosomes (type: Int64, default: 1)
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-t, --tempdirectory TEMPDIRECTORY
tempdirectory directory for intermediate
results (default: tempdir())
--nplot_subpop NPLOT_SUBPOP
plots for up to nplot_subpop offspring in each
subpopulation (type: Int64, default: 10)
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit
rabbit_thinancestry.jl
julia rabbit_thinancestry.jl -husage: rabbit_thinancestry.jl -g ANCESTRYFILE [--thincm THINCM]
[-o OUTSTEM] [-w WORKDIR] [-h]
Reduce ancestry results on a subset of markers such that inter-marker
distances <= thincm.
optional arguments:
-g, --ancestryfile ANCESTRYFILE
anncestry file resulting from magicreconstruct
--thincm THINCM keep ancestry results on a subseut of markers
such that inter-marker distances <= thincm. By
default, thincm=0, keeping only the first of
markers at the same position. (type: Float64,
default: 0.0)
-o, --outstem OUTSTEM
outstem of output files (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-h, --help show this help message and exit
rabbit_magicscan.jl
julia rabbit_magicscan.jl -husage: rabbit_magicscan.jl -g ANCESTRYFILE -p PHENOFILE [-e EQUATION]
[--thresholds THRESHOLDS] [--nperm NPERM]
[--siglevels SIGLEVELS] [--islog10p ISLOG10P]
[--missingstring MISSINGSTRING]
[--commentstring COMMENTSTRING] [-o OUTSTEM]
[-w WORKDIR] [-v VERBOSE] [-h]
Genomic scan of QTLs in connected multiparental populations
optional arguments:
-g, --ancestryfile ANCESTRYFILE
ancestry file resulting from
`magicreconstruct`
-p, --phenofile PHENOFILE
phenotypic data file
-e, --equation EQUATION
equation from linear model. If it is nothing,
last_colname ~ 1 (default: "nothing")
--thresholds THRESHOLDS
list of thresholds for QTL detection. e.g,
"[4.0]". (default: "nothing")
--nperm NPERM number of permutations of phenotypes for
calculating unspecified thresholds (type:
Int64, default: 200)
--siglevels SIGLEVELS
significance levels for calculating thresholds
by permutations, e.g, "[0.05, 0.10]".
(default: "[0.05]")
--islog10p ISLOG10P if islog10p = true, profile refers to -log10
P-value, and otherwise LOD score (type: Bool,
default: false)
--missingstring MISSINGSTRING
string denotes a missing phenotypic value
(default: "NA")
--commentstring COMMENTSTRING
rows that begin with commentstring will be
ignored (default: "##")
-o, --outstem OUTSTEM
stem of output filenames (default: "outstem")
-w, --workdir WORKDIR
directory for reading and writing files
(default: pwd())
-v, --verbose VERBOSE
if true, print messages on console (type:
Bool, default: true)
-h, --help show this help message and exit