PSEQ command/option reference table

Command Options Description
append add a file to the project --file { str-list } generic input file(s)
--name { str-list } generic name(s) variable
--type { str } type of project entry
assoc gene-based association tests --fix-null { flag } exclude individuals with null genotypes
--info { flag } report ISTAT in association test
--midpoint { flag } report interval BP mid-point in output
--perm { int } number of permutations
--phenotype { str-list } phenotype specification
--tests { keyword } gene-based tests
calpha { flag } c-alpha test
fw { flag } frequency-weighted test
no-burden { flag } do not apply basic burden test
sumstat { flag } sum-statistic test
uniq { flag } burden of case-unique variants
vt { flag } variable threshold test
attach-meta load meta-information for existing VARDB variants --file { str-list } generic input file(s)
--group { str-list } generic group label(s)
--id { int-list } generic numeric IDs
clusters .
commands list commands/groups
concordance genotypic concordance checks --report-all { flag } .
counts summary/count statistics --name { str-list } generic name(s) variable
--output-vcf { flag } summary counts in VCF format
delete-meta remove meta-information --group { str-list } generic group label(s)
denovo filter for de-novo mutations --param { float-list } parameter list
drop drop a file from the project --file { str-list } generic input file(s)
--name { str-list } generic name(s) variable
--type { str } type of project entry
file-summary summary of project files --ugly { flag } do not format summary output
g-counts genotype summary/count statistics --name { str-list } generic name(s) variable
--output-vcf { flag } summary counts in VCF format
g-matrix write a matix of gene-based allele counts --collapse { flag } .
--hide-invariant { flag } .
g-meta-matrix matix of gene-based per-individual meta-information --name { str-list } generic name(s) variable
g-stats gene-based summary statistics --stats { keyword } quantitaties calculated under (v|g|i)-stats
g-view view variants grouped by gene --geno { flag } show genotypes
--gmeta { flag } show genotype meta-information
--phenotype { str-list } phenotype specification
--rarelist { flag } rare-list mode for v-view
--transpose { flag } transposed g-view output
--verbose { flag } verbose output
--vmeta { flag } show variant meta-information
glm general linear models --covar { str-list } covariate(s)
--perm { int } number of permutations
--phenotype { str-list } phenotype specification
--show-covar { flag } list coefficients for covariates
--use-dosages { str } genotypes are dosages in specified tag
--use-postprobs { str } genotype are posterior probabilities in specified tag
--vmeta { flag } show variant meta-information
group-comparison .
gs-view view gene variants in sequence --ref-variants { str } .
i-stats per-individual statistics --stats { keyword } quantitaties calculated under (v|g|i)-stats
i-view individuals in project/file --from-vardb { flag } list individuals from VARDB, not INDDB
--pheno .
ibd-load load IBD segment data --file { str-list } generic input file(s)
--ibddb { str } IBD segment database location
ibd-sharing pairwise IBD sharing around rare variants --ibddb { str } IBD segment database location
ibs-matrix IBS matrix calculation --long-format { flag } output one row per line (instead of n-by-n matrix)
--two-counts { flag } only consider variants seen twice in the sample
ind-summary summary of INDDB --ugly { flag } do not format summary output
index-bcf add index to VARDB for a BCF --bcf { str-list } BCF file locations
index-vcf add index to VARDB for a BGZF-compressed VCF --vcf { str-list } VCF file locations
intersect intersect locus groups --file { str-list } generic input file(s)
--group { str-list } generic group label(s)
load-pedigree load pedigree information into INDDB --file { str-list } generic input file(s)
load-pheno load phenotypes into INDB --file { str-list } generic input file(s)
load-plink load a PLINK binary PED file (BED) --check-reference { flag } loading/indexing VCFs, report if REF != SEQDB
--fid { flag } use FID as ID when reading PLINK files
--file { str-list } generic input file(s)
--fix-strand { flag } fix strand given a SEQDB when loading a PLINK GWAS file
--id { int-list } generic numeric IDs
--iid { flag } use IID as ID when reading PLINK files
load-vcf load all VCF files not already in VARDB --exclude-meta .
--file { str-list } generic input file(s)
--filter { str } loading VCF, only load variants in specified LOCDB group
--include-meta .
--vcf { str-list } VCF file locations
load-weights load weight table --file { str-list } generic input file(s)
--name { str-list } generic name(s) variable
loc-annotate annotate loci --group { str-list } generic group label(s)
--show-subregions { flag } modifies loc-view output
loc-delete remove a LOCDB group --group { str-list } generic group label(s)
loc-delete-alias remove gene-alias table
loc-delete-special remove all special variables from a LOCDB
loc-drop-index remove index from LOCDB
loc-get-special get special variable(s) from a LOCDB --key { str } key of key-value pair
loc-index index a LOCDB
loc-intersect view loci from a LOCDB group with 1 or more variants
loc-load load from a .GTF or .REG file into LOCDB --file { str-list } generic input file(s)
--group { str-list } generic group label(s)
--keep-unmerged { flag } retain unmerged region group when loading GTF
loc-load-alias load a gene-alias table --file { str-list } generic input file(s)
loc-merge merge a LOCDB group --group { str-list } generic group label(s)
loc-overlap show loci in groups Y, Z that overlap each locus in X --alias { str-list } locus alias group(s)
--comma .
--group { str-list } generic group label(s)
--row .
--tab .
loc-set-special set special variable in a LOCDB --key { str } key of key-value pair
--value { str-list } value(s) of key-value pair
loc-stats locus-based stats --loc-group { str } LOCDB group label
--no-subregions { flag } modifies loc-view output
--ref-group { str } REFDB group label
--show-subregions { flag } modifies loc-view output
loc-summary summary of LOCDB --ugly { flag } do not format summary output
loc-swap-names swap LOCDB names --alternate-name { flag } use LOCDB alternate name (e.g. gene symbol)
--file { str-list } generic input file(s)
--group { str-list } generic group label(s)
loc-translate AA sequence of loci
loc-update-name-table update LOCDB name table --alternate-name { flag } use LOCDB alternate name (e.g. gene symbol)
--group { str-list } generic group label(s)
--index-name { flag } use LOCDB primary/index name (e.g. transcript ID)
loc-view show all loci in a LOCDB group --alias { str-list } locus alias group(s)
--group { str-list } generic group label(s)
--no-meta { flag } do not show locus meta-information
--show-subregions { flag } modifies loc-view output
locset-load load a locus-set --alternate-name { flag } use LOCDB alternate name (e.g. gene symbol)
--file { str-list } generic input file(s)
--group { str-list } generic group label(s)
--name { str-list } generic name(s) variable
lookup lookup various annotatations for a list of positions --alias { str-list } locus alias group(s)
--annotate { str } annotate variants
--loc { str-list } transcript group
--ref { str-list } reference-variant group
masks list mask options
meta-matrix write a matrix of variant meta-information
meta-summary summary of variant meta-information --ugly { flag } do not format summary output
mrv-view view multiple rare variants
mutation-screen screen for new mutations given shared IBD --ibddb { str } IBD segment database location
--indiv { str-list } specify individual(s)
--region { str-list } region(s)
mv-view view multiple variants
net-assoc network-based gene-association --file { str-list } generic input file(s)
--netdb { str } network database location
--output { keyword } general output format modifiers
--pheno .
net-load populate a NETDB --file { str-list } generic input file(s)
--netdb { str } network database location
net-view view gene connections in a NETDB --group { str-list } generic group label(s)
--name { str-list } generic name(s) variable
--netdb { str } network database location
new-project set a new project --inddb { str } individual database location
--locdb { str } locus database location
--metameta { str } meta-information meta-information
--output { keyword } general output format modifiers
--refdb { str } reference database location
--resources { str } central resource folder
--scratch { str } scratch folder
--seqdb { str } sequence database location
--vardb { str } variant database location
--vcf { str-list } VCF file locations
proximity-scan VCF --distance { flag } .
ref-load load data (VCF or flat-file) into REFDB --file { str-list } generic input file(s)
--group { str-list } generic group label(s)
--vcf { str-list } VCF file locations
ref-summary summary of REFDB --ugly { flag } do not format summary output
ref-view view a group from a REFDB --group { str-list } generic group label(s)
--vmeta { flag } show variant meta-information
reload-vcf clear VARDB, then reload all VCF (not implemented yet)
rv-view view rare alleles --pheno .
s-assoc segment-based IBD test --file { str-list } generic input file(s)
--perm { int } number of permutations
score-weights score variants for weights --name { str-list } generic name(s) variable
seg-summary summary of SEQDB --ugly { flag } do not format summary output
seg-view individual segments --group { str-list } generic group label(s)
seq-load load FASTA into SEQDB --. .
--description { str } file description
--file { str-list } generic input file(s)
--format { keyword } .
build { str } .
iupac { flag } .
repeat-mode { str } .
--name { str-list } generic name(s) variable
seq-summary summary of SEQDB --ugly { flag } do not format summary output
seq-view view regions of sequence from SEQDB --compact { flag } compact seq-view output
--region { str-list } region(s)
set-enrich test per individual for greater-than-expected burden of variants per set --locset { str-list } locus-set group
--perm { int } number of permutations
--phenotype { str-list } phenotype specification
simple-sim simple gene variant simulation
summary summary of all databases --ugly { flag } do not format summary output
tag-file add file-tags to VARDB --id { int-list } generic numeric IDs
--name { str-list } generic name(s) variable
unique view variants specific to individual groups --allow { int } allow N individuals without variant
--indiv { str-list } specify individual(s)
--require { int } require N individuals with variant
v-assoc single-variant association --fix-null { flag } exclude individuals with null genotypes
--info { flag } report ISTAT in association test
--perm { int } number of permutations
--phenotype { str-list } phenotype specification
--separate-chr-bp { flag } report CHR-tab-BP not chr:BP
--vmeta { flag } show variant meta-information
v-dist comparison of rare-variant group distributions --perm { int } number of permutations
--whole-sample-counts { flag } .
v-freq variant frequency data --em { float } EM calculation of P(geno|data) from GL or PL
v-matrix write a matrix of allele counts
v-meta-matrix write a matrix of individual genotype meta-information --name { str-list } generic name(s) variable
v-stats variant statistics --stats { keyword } quantitaties calculated under (v|g|i)-stats
count { str-list } arbirary tag range counts
dp { int-range-vector } variant read-depth counts
gcount { str-list } genotype tag range counts
gmean { str-list } genotype tag means
hwe { float-range-vector } HWE test p-values
mac { int-range-vector } MAC range counts
maf { float-range-vector } MAF range counts
mean { str-list } arbitrary mean tag values
qual { float-range-vector } QUAL range counts
v-view view variant data --geno { flag } show genotypes
--gmeta { flag } show genotype meta-information
--hide-null { flag } .
--only-alt { flag } .
--only-minor { flag } .
--pheno .
--samples { flag } show each specific sample variant
--simple { flag } simple variant format, POS RET ALT
--verbose { flag } verbose output
--vmeta { flag } show variant meta-information
vacuum clean-up unused disk-space in VARDB
var-delete remove file from VARDB --id { int-list } generic numeric IDs
var-drop-all-sets drop all sets from a VARDB
var-drop-all-supersets drop all supersets from a VARDB
var-drop-set drop a set from a VARDB
var-drop-superset drop a superset from a VARDB
var-set add a variant-set to a VARDB --file { str-list } generic input file(s)
--group { str-list } generic group label(s)
var-summary summary of VARDB --ugly { flag } do not format summary output
var-superset add a super-set to a VARDB --file { str-list } generic input file(s)
--group { str-list } generic group label(s)
--members { str-list } super-set members
version display version information
write-bcf output from VARDB to BCF --bcf { str-list } BCF file locations
write-haps write a MaCH format haplotype file
write-lik write a BEALGE likelihood file
write-ped write a new PLINK TPED fileset --name { str-list } generic name(s) variable
--use-family-id .
write-vardb write a new VARDB --new-project { str } new project specification filename
--new-vardb { str } new VARDB name, for write-vardb

PSEQ Options Reference

Auxillary option Abbreviation Description
--help Produce a help message
--vcf VCF file locations
--bcf BCF file locations
--resources Central resource folder
--scratch Scratch folder
--metameta Meta-information meta-information
--vardb Variant database location
--inddb Individual database location
--refdb Reference database location
--seqdb Sequence database location
--segdb Segent database location
--locdb Locus database location
--file Generic input file(s)
--group Generic group label(s)
--region Region(s)
--alias Locus alias group(s)
--name Generic name(s) variable
--type Type of project entry
--id Generic numeric IDs
--options Context-specific options
--output Output folder
--whitespace Allow whitespace delimited input
--debug Set debug mode
--silent Set silent mode
--ignore-warnings Turn off warnings
--out-file Set main output file
--out-file Debug file name
--prolix-file Prolix output filename
--long Set long output mode
--long-header Set header/long output mode
--mask Mask specification
--gene gene-group gene1 gene2 …
--hide Hide specific meta-fields
--show Show specific meta-fields
--vmeta Show variant meta-information
--samples Show specific sample variants in v-view
--verbose Verbose output
--geno Show genotypes (g-view)
--gmeta Show genotype meta-information
--transpose Transposed g-view output
--variant Show specific variant (v-view)
--indiv Specify individual(s)
--annot Transcript(s) group for annotation
--phenotype Phenotype specification
--make-phenotype Dichotomise factor
--strata Stratifier variable
--covar Covariate(s)
--perm Number of permutations
--a-perm Adaptive perm min, max

PSEQ Mask Reference

Mask option Description
var
var.subset
var.skip
var.ex
var.req
loc
loc.subset
loc.skip
loc.ex
loc.req
gene
locset
locset.subset
locset.skip
locset.ex
locset.req
ref
ref.ex
ref.req
file
file.ex
obs.file
obs.file.req
obs.file.ex
alt.file
alt.file.req
alt.file.ex
alt.group
alt.group.req
alt.group.ex
obs.nfile
alt.nfile
fail.nfile
reg
reg.ex
reg.req
filter
filter.ex
filter.req
any.filter
any.filter.ex
any.filter.req
biallelic
biallelic.ex
monomorphic
monomorphic.ex
meta.attach
meta
meta.req
geno
geno.req
mac
hwe
maf
null
qual
assume-ref
downcode
collapse
overlap-merge
case.control
case.uniq
control.uniq
em
var.append
loc.append
locset.append
ref.append
annot
annot.ex
annot.req
annot.append
indiv
indiv.ex
phe.obs
phe.allowe.missing
phe
phe.ex
phe.req
var.group
loc.group
reg.group
locset.group
fail.single.file
empty.group
limit
v-include
ex-vcf