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| readme.qcf90 [2019/03/06 23:33] – [Manual] yutaka | readme.qcf90 [2022/05/30 21:34] – [Long-help] andres |
|---|
| ===== Manual ===== | ===== Manual ===== |
| |
| * [[http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=pdf:manual_qc.pdf|QCF90 Draft Manual]] (updated on March 6, 2018) | * [[http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=pdf:manual_qc.pdf|QCF90 Draft Manual]] (updated on November 3, 2020) |
| |
| | ===== 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> |
