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readme.qcf90 [2020/01/25 01:47] – [Manual] yutaka | readme.qcf90 [2024/03/25 18:22] (current) – external edit 127.0.0.1 |
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===== Manual ===== | ===== Manual ===== |
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* [[http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=pdf:manual_qc.pdf|QCF90 Draft Manual]] (updated on January 24, 2020) | * [[http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=pdf:manual_qc.pdf|QCF90 Draft Manual]] (updated on November 3, 2020) |
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| ===== 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> |