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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 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> |