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.

• QCF90 Draft Manual (updated on November 3, 2020)

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