Usage: qctool OPTIONS: Input file options: -filetype : Specify the filetype of the genotype files specified by -g. By default, qctool will guess the file type. Use this option to override that guess. Possible types are: "gen","bgen","v- cf","hapmap_haplotypes","impute_haplotypes","shapeit_haplotypes". -g : Path of gen file(s) to input. The given filename may contain the wildcard character '#', which expands to match aone- or two-character chromosome identifier. (For example, "qcto- ol -g myfile_#.gen" will match "myfile_1.gen", "myfile_2.gen", etc., or "myfile_01.gen", "myfile_02.gen", etc.) Only human autosomes are matched this way. This option may also be repeated, in which case each invocation is treated as a seperate cohort and cohorts are joined together to create one big dataset. -s : Path of sample file to input. If specified, this option must occur as often as the -g op- tion to specify one sample file per cohort. Sample exclusion options: -excl-samples : Filter out samples whose sample ID lies in the given file. -incl-samples : Filter out samples whose sample ID does not lie in the given file(s). SNP exclusion options: -excl-positions : Exclude all SNPs whose position is in the given file(s) from the analysis. Positions shou- ld be in the form [chromosome]:[position] and separated by whitespace. -excl-range : Specify a range of SNPs (or space-separated list of ranges of SNPs) to exclude from opera- tion. Each range should be in the format CC:xxxx-yyyy where CC is the chromosome and xxxx and yyyy are the start and end coordinates, or just xxxx-yyyy which matches that range fr- om all chromosomes. You can also omit either of xxxx or yyyy to get all SNPs from the sta- rt or to the end of a chromosome. -excl-rsids : Exclude all SNPs whose RSID is in the given file(s) from the analysis. -excl-snpids : Exclude all SNPs whose SNPID is in the given file(s) from the analysis. -excl-variants : Exclude all SNPs in the given file(s) from the analysis. The format of this file is the s- ame as that output by the -write-snp-excl-list option. It must have six columns interpre- ted as SNPID, rsid, chromosome, position, first and second alleles. -excl-variants-matching : Filter out snps whose rsid or SNPID matches the given value. The value should be a string which can contain a % wildcard character (which matches any substring). Optionally, prefi- x the argument with snpid~ or rsid~ to only match against the SNPID or rsid fields. -incl-positions : Exclude all SNPs whose position is not in the given file(s) from the analysis. Positions should be in the form [chromosome]:[position] and separated by whitespace. -incl-range : Specify a range of SNPs (or space-separated list of ranges of SNPs) to operate on. Each r- ange should be in the format CC:xxxx-yyyy where CC is the chromosome and xxxx and yyyy ar- e the start and end coordinates, or just xxxx-yyyy which matches that range from all chro- mosomes. You can also omit either of xxxx or yyyy to get all SNPs from the start or to th- e end of a chromosome. -incl-rsids : Exclude all SNPs whose RSID is not in the given file(s) from the analysis. -incl-snpids : Exclude all SNPs whose SNPID is not in the given file(s) from the analysis. -incl-variants : Exclude all SNPs not in the given file(s) from the analysis. The format of this file is t- he same as that output by the -write-snp-excl-list option. It must have six columns inte- rpreted as SNPID, rsid, chromosome, position, first and second alleles. -incl-variants-matching : Filter out snps whose rsid or SNPID does not match the given value. The value should be a string which can contain a % wildcard character (which matches any substring). Optionally, prefix the argument with snpid~ or rsid~ to only match against the SNPID or rsid fields. Options for adjusting SNPs: -assume-chromosome : Treat each SNP whose chromosome cannot be determined as though it lies on the specified c- hromosome. -match-alleles-to-cohort1: Specify that alleles (and corresponding genotypes) in all cohorts should be switched, if necessary, so as to match the alleles of the first cohort. -compare-variants-by : By default, matching SNPs between cohorts uses all the available fields (position, rsid, SNPID, and alleles.) Use this option to specify a comma-separated subset of those fields to use instead. The first entry must be "position". This option can be used, for example, when cohorts are typed on different platforms so have different SNPID fields. Defaults t- o "position,rsid,SNPID,alleles". Output file options: -og : Specify that qctool should write an output genotype file with the specified filename. The type of this file will be determined from the filename extension. If the first occurence of -g uses a '#' wildcard character, the '#' character can also be used here to specify n- umbered output files corresponding to the input files.If "-" is specifed here, genotypes are written to standard output in GEN format. -omit-chromosome: (This option is specific to output files in the GEN format.) Do not output a chromosome c- olumn. -os : Output sample information to the file specified. -sort: Sort the genotypes in the output file. Currently this is only supported if BGEN, unzippe- d GEN, unzipped VCF format is output. VCF file options: -metadata : Specify the name of a file containing VCF metadata to be used to parse a VCF file. Keys in this file must either not be present in the VCF file, or must have identical values. -vcf-genotype-field : Specify the name of the field in a VCF file to read genotypes from. This must match the name of a FORMAT field in the VCF file. Defaults to "GT". Statistic calculation options: -sample-stats : Calculate and output sample-wise statistics. -snp-stats : Calculate per-SNP summary statistics and store them in the specified file. (This implies that no SNP filtering options are used.) SNP filtering options: -hwe : Filter out SNPs with -log10( HWE p-value ) greater than or equal to the value specified. -info : Filter out SNPs with Fisher information lying outside the given range. -maf : Filter out SNPs whose minor allele frequency lies outside the interval [a,b]. -snp-missing-call-rate : Filter out SNPs with missing call rate greater than or equal to the value specified. -snp-missing-rate : Filter out SNPs with missing data rate greater than or equal to the value specified. Sample filtering options: -heterozygosity : Filter out samples with heterozygosity (as taken from the "heterozygosity" column of the sample file, which must be present) outside the interval [a,b]. -sample-missing-rate : Filter out samples with missing data rate (as taken from the "missing" column of the samp- le file) greater than the value specified. Inclusion / exclusion list options: -write-sample-excl-list : Write a file containing a list of the ids of individuals which are filtered out by the sa- mple filter. -write-snp-excl-list : Write a file (or files) containing the SNPs that are filtered out. Other options: -force: Ignore warnings and proceed with requested action. -log : Specify that qctool should write a log file to the given file. Options for adjusting sample data: -condition-on : Condition on the dosages of a given SNP or set of SNPs. The argument should be a comma-se- parated list of values of the form: [field]~[value]:[dose][,dose...] where field is "rsid", "snpid", or "pos", value is the value to match, and each dose is o- ne of add,dom,het,rec,or gen. If the field is omitted, it is assumed to be rsid; if the d- ose is omitted it is assumed to be add. -missing-code : Specify a comma-separated list of strings to be treated as missing values when encountere- d in the sample file(s). Defaults to "NA". -quantile-normalise : Quantile normalise each specified continuous phenotype or covariate by ranking its values and mapping to quantiles of the standard normal distribution N(0,1). Ties are handled by sending tied values to the average of the corresponding quantiles.The argument should be a comma-separated list of column names from the sample file. Test / benchmark options: -read-test: Don't do anything; just read the data.