Produced by " -recode beagle", for use by BEAGLE. chr-*.map (BEAGLE unphased genotype and variant information files) Cannot currently be generated by PLINK use " -recode vcf" to produce a VCF file for now. Variant information + sample ID + genotype call binary file, loaded with -bcf. Lines are permitted to contain different numbers of fields.bcf (1000 Genomes Project binary Variant Call Format, version 2) Subsequent fields are defined by the plugin function. Allele 1 (corresponding to allele counts in GENO matrix usually minor).Refer to the PLINK 1.07 documentation for more (R plugin function results)Ī text file with no header line, and one line per variant, each with at least four fields. Standard error of beta (log-odds) estimateīottom of xy% symmetric approx. xy has also been specified, the following three fields are inserted before 'STAT': SE Regression coefficient (-linear, "-logistic beta") or odds ratio (-logistic without 'beta') Number of observations (nonmissing genotype, phenotype, and covariates) Not present with 'no-snp'.Īllele 1 (usually minor). Not present with 'no-snp'.īase-pair coordinate. assoc.logistic (multi-covariate association analysis report)Ī text file with a header line, and T lines per variant typically with the following nine fields (where T is normally the number of terms, but the 'genotypic' and 'hethom' modifiers and the -tests flag can change this): CHRĬhromosome code. (Unless the phenotype is quantitative instead of case/control then phenotypes are ignored and FRQ_A and FRQ_U are both equal to the overall FRQ value.). If the 'case-control-freqs' modifier is present, the FRQ column is replaced with FRQ_A and FRQ_U columns reporting case and control frequencies, respectively, and NCHROBS will not include missing-phenotype samples.
Standard error of effect (not odds ratio) estimate Regression coefficient (for quantitative traits) or odds ratio R-squared quality metric/information content assoc.dosage (dosage association analysis report)Ī text file with a header line, and then usually one line per variant with the following 8-10 fields: CHR xy has also been specified, there are three additional fields at the end: SEīottom of xy% symmetric approx. If the 'counts' modifier is present, the 5th and 6th fields are replaced with: C_A
Odds(allele 1 | case) / odds(allele 1 | control) Not present with 'fisher'/'fisher-midp' modifier. Produced by -assoc acting on a case/control phenotype.Ī text file with a header line, and then one line per variant typically with the following 9-10 fields: CHRĪllelic test chi-square statistic. assoc.fisher (case/control association allelic test report) Expected allele #1 (from -update-alleles input file).Produced by -update-alleles when there is a mismatch between the loaded alleles for a variant and columns 2-3 of the -update-alleles input file.Ī text file with no header line, and one line per mismatching variant with the following three fields: (As a result, if the QQ field is present, its values just increase linearly.). Variants/sets are sorted in p-value order. Only present with 'qq-plot' modifier.īenjamini & Hochberg (1995) step-up false discovery controlīenjamini & Yekutieli (2001) step-up false discovery control Not present with set tests.ĭevlin & Roeder (1999) genomic control corrected p-value. *.adjusted (basic multiple-testing corrections)Ī text file with a header line, and then one line per set or polymorphic variant with the following 8-11 fields: CHRĬhromosome code. (Most extensions not listed here have very simple one-entry-per-line text formats.) This page describes specialized PLINK input and output file formats which are identifiable by file extension.
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