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PEDSTATS -- Program Options
Input Files and Basic Parameters
-d datafile - Selects input data file, in LINKAGE, QTDT or MENDEL format.
-p pedfile - Selects pedigree file, with genotype, phenotype and family structure information.
-i ibdfile - Selects IBD sharing file. See section on IBD sharing for further details.
-a pdffile - Send Adobe PDF format output to pdffile instead of the default pedstats.pdf
-x missing_value_code -
Selects the missing value code for quantitative phenotypes and covariates in the pedigree file. If possible, it is always safer
to replace missing values with 'x', rather than use this option.
Additional options
Pedigree File
The following options allow fine control over processing of pedigree files:
--ignoreMendelianErrors -
Calculate statistics even if Mendelian inconsistencies are present in the pedigree. The
default behavior is to list inconsistencies and stop.
--chromosomeX -
Calculate statistics for X-linked loci. In this case, males are hemizygous and carry only
one chromosome. In the pedigree file they should be encoded as if they carried two identical
alleles.
--trim -
Remove uninformative individuals from pedigree before calculating statistics. This option can
be combined with the --rewritePedigree option below. Uninformative individuals are
individuals with no genotype or phenotype data who are not required to establish relationships
between individuals for whom data is available.
Genotype Checks
The following options control tests for Hardy-Weinberg Equilibrium, which can be
used to identify problems with genotype data or pedigree formatting. When PDF output is also requested, graphical summaries
of Hardy-Weinberg tests are produced for each marker.
--hardyWeinberg -
This option runs two sets of tests for Hardy-Weinberg equilibrium, one among all individuals in
the pedigree file and another among a set of unrelated individuals.
--showAll -
Print non-significant results for Hardy-Weinberg equilibrium tests. The default
behavior for Hardy-Weinberg test options is to report only significant results.
--cutoff -
This option sets the significance cutoff for graphical and text display of Hardy-Weinberg test results.
The default behaviour is to report results for tests with p < 0.05.
Hardy Weinberg Sample
--checkUnrelated -
This option runs the Hardy-Weinberg equilibrium test using genotypes from a set of unrelated individuals.
Pedstats selects a set of unrelated individuals from your data that will almost always include more
independent genotypes per marker than a founders only test. Individuals chosen for the test set
are reported in the file (pedstats.hweselection). For details of the selection algorithm
see our description of Hardy-Weinberg testing in unrelated samples .
--checkAll -
This option runs the Hardy-Weinberg equilibrium test using all genotypes. As implemented, this test
ignores family structure but can be useful when the pool of individuals chosen by the unrelated sample
test is small or mostly ungenotyped for one or more markers.
--checkFounders -
This option runs the Hardy-Weinberg equilibrium test using only founder genotypes.
Age Checking
These options control checking of age variables for inappropriate pairwise values (e.g a father-son
pair where the son is reported to be older than the father, a twin pair with different ages, etc)
--age -
This option specifies the label (as written in the dat file) for an age variable.
--birth -
This option specifies the label (as written in the dat file) for a birth year variable.
Generation
These options control allowable gaps for checks of age and birth year variables.
--minGap -
This option specifies the minimum allowable generation gap. Differences
in parent-offspring ages or birth year that imply a shorter generation gap will be flagged as
an error when age checks are run.
--maxGap -
This option specifies the maximum allowable generation gap. Differences
in parent-offspring ages or birth year that imply a longer generation gap will be flagged as
an error when age checks are run.
--sibGap -
This option specifies the maximum allowable gap in age or birth year among siblings. Differences
in ages or birth year that imply a longer gap between siblings will be flagged as
an error when age checks are run.
Output Options
These options request generation of additional output.
--pairs -
Count the number of sib, parent-offspring, avuncular, grandparent-grandchild and cousin pairs in the
pedigree. For each dichotomous trait, count affected, unaffected, and discordant diagnosed pairs. For covariates and
quantitative traits, provide correlations and counts of phenotyped pairs for each relative pair type. When this option is used in
conjunction with the --pdf, option, a graphical summary of pairwise data is also provided.
--rewritePedigree -
Rewrite pedigree after re-organizing families into connected groups of individuals and trimming
uninformative individuals (if the --trim command line switch is set).
--verbose -
Report family and person ids for group members when disconnected family groups are detected within a single family.
--markerTables -
Report summary tables for marker heterozygosity and genotyping
rates. When this option is selected, detailed marker information and
Hardy-Weinberg test results are redirected to a separate text file (pedstats.markerinfo). For datasets
including
more than 50 marker genotypes, this option is automatically selected.
Grouping options
These options control additional reporting of summary statistics by group.
--byFamily - Break down text output by family. When this option is specified,
each type of text summary is written on
a per family basis to a separate text file with naming convention pedstats.*.fam, where * identifies the
type of summary. For instance, covariate summaries by family be will written to a separate text file called
pedstats.cov.fam.
--bySex -
Break down text output by sex; when using --pdf or --pairs options, produce sex-specific
summaries of affection and trait variables
Options for PDF Output
--pdf - Generate charts summarizing contents of pedigree file in Adobe PDF format.
--markerPDF - Generate PDF output only for markers.
--familyPDF - Generate PDF ouput only for family information.
--traitPDF - Generate PDF output only for traits and covariates.
--affPDF - Generate PDF output only for affection variables.
Options for pedigree filtering
These options specify criteria for inclusion in the pedigree sample. Any individual not meeting
these criteria is removed from the pedigree sample before any summaries are created.
--minGenos:val - Remove individuals from pedigree sample that have fewer than
val genotyped markers
--minPhenos:val - Remove individuals from pedigree sample that have fewer than
val phenotyped traits
--minCovariates:val - Remove individuals from pedigree sample that have fewer than
val measured covariates
--affectedFor:aff_var - Remove individuals from pedigree sample that are unaffected or have not been diagnosed for the
affection variable aff_var.
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