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readme.qcf90 [2019/03/06 23:33]
yutaka [Manual]
readme.qcf90 [2022/05/30 21:34] (current)
andres [Long-help]
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 ===== Manual ===== ===== Manual =====
  
-   * [[http://​nce.ads.uga.edu/​wiki/​lib/​exe/​fetch.php?​media=pdf:​manual_qc.pdf|QCF90 Draft Manual]] (updated on March 62018)+   * [[http://​nce.ads.uga.edu/​wiki/​lib/​exe/​fetch.php?​media=pdf:​manual_qc.pdf|QCF90 Draft Manual]] (updated on November 32020)
  
 +===== Long-help =====
 +
 +<​file>​
 +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
 + </​file>​
readme.qcf90.1551915180.txt.gz ยท Last modified: 2019/03/06 23:33 by yutaka