UNDER CONSTRUCTION
This is a quality-control tool for genotypes and pedifree. It supports non-renumbered files; you can use this tool before running renumf90.
This is qcf90, Version 1.2.0. with zlib
Yutaka Masuda, Ignacio Aguilar, Andres Legarra, and Ignacy Misztal
University of Georgia
usage: qcf90 [options]
Options:
Source file specification
--snpfile mfile marker file
--snpfile-header n skip first n lines as header
--mapfile cfile read map file
--maffile ffile read MAF file
--pedfile pfile pedigree file
--xrefid xfile XrefID file; assumed renumbered pedigree
--statfile qfile read QC status from a file instead of computing
Marker quality-control (QC) options
--qc {items} * quality control; see --long-help for details
--crm n call rate for markers; default=0.90
--cra n call rate for animals; default=0.90
--maf n minimum allele frequency; default=0.05
--hwe n check for Hardy-Weinberg equilibrium
--trio Mendelian check with sire-dam-progeny combination
--skip-marker-list file marker positions to be skipped (temporarily excluded) in QC
--skip-animal-list file animal ID (same as pedigree if supplied) to be skipped in QC
--exclude-marker-list file marker positions to be removed immediately
--exclude-animal-list file animal ID to be removed immediately
--remove-markers * remove unqualified markers in subsequent QC steps
--remove-animals * remove unqualified animals in subsequent QC steps
--check-parentage check Mendelian inconsistency; equivalent to --qc par
--check-format * check file format precisely
--outcallrate save detailed call rate for markers and animals
--number_parent_progeny_evaluations n minimum pair of parent-progeny conflicts
--exclusion_threshold n error rate for parent-progeny in parentage
--exclusion_threshold_snp n error rate for markers in parentage
--outparent_progeny save all parent-progeny comparisons
--out_snp_exclusion_error_rate save all Mendelian conflicts for markers
Genomic identity checks
--check-identity [file] check identical genotypes; compare within snpfile if no [file] specified
--threshold-identity n criteria of identity = #matched/#compared excluding missing
--random-markers-identity n use random n markers for identity checks
--fixed-markers-identity file use a subset of markers in the file for identity checks
--save-markers-identity save the randomly sampled markers used in identity checks
Marker options
--sex-chr n.. sex chromosome ID(s)
--skip-chr n.. chromosome ID(s) to be skipped in QC
--exclude-chr n.. chromosome ID(s) to be removed immediately
Pedigree options
--ped-position a,s,d position of animal, sire, and dam ID; default=1,2,3
--upg type definition of unknown parents groups (default="zero+negative")
Job control and performance options
--script file read options from the file; overwritten with command-line options
--halt-on-warning stop on warning (default: keep going with minor issues)
--dry-run show tasks to be performed; no computations
--fastread read marker files quickly
--marker-storage {type} format on memory storage; type={pack,int,real} default=pack
--gzip-level gzip compression level
--num-threads n number of threads used for OpenMP; default=1
File output options
--save-log [file] * save log file; default=qcf90.log
--save-status [file] * save QC status; default=qcf90.status
--save-dot [file] * save dot file to visualize pedigree loops; default=pfile+".dot"
--save-clean [suffix] save qualified files with the suffix; default="_clean"
--cleanup-marker-flags n.. flags for markers being removed from clean files; default=all
--cleanup-animal-flags n.. flags for animals being removed from clean files; default=all
Miscellaneous options
--debug n set debug level to n (default=0)
--version show version
--help show help
--long-help show help, all options, and details
Quality control options: --qc {crm,maf,mono,hwe,cra,par,h2gc}
* crm call rate for markers
* maf minor allele frequency
* mono monomorphic markers
* hwe Hardy-Weinberg equilibrium
* cra call rate for animals
* par parentage (Mendelian inconsistency) for markers and animals
* h2gc heritability of gene content
* Set by default. Turn off the option by putting --no- as a prefix instead of --.
For example, use --no-check-format to avoid checks for the file format.
Default criteria/threshold for quality control:
crm call rate for markers: 0.900
maf minor allele frequency: 0.050
mono monomorphic markers: 0 or 1
hwe Hardy-Weinberg deviations
abs(observed - expected heterozygotes): 0.150
cra call rate for animals: 0.900
par parentage for markers and animals
# of markers needed: 100
error rate for animals: 0.010
error rate for markers: 0.100
identity of genotypes: 0.990